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However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c00352","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T10:53:23Z","timestamp":1781520803000},"page":"9057-9075","source":"Crossref","is-referenced-by-count":0,"title":["Assessing Metal\nIon Assignment Accuracy in Protein\nData Bank Models via Elemental Spectroscopy"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8714-3191","authenticated-orcid":true,"given":"Edward H.","family":"Snell","sequence":"first","affiliation":[{"name":"SUNY University at Buffalo , , 120 Bonner Hall , , ,","place":["Buffalo, New York, United States, 14260"]},{"name":"The University at Buffalo Hauptman-Woodward Institute , 700 Ellicott St. , , ,","place":["Buffalo, New York, United States, 14203"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4957-8175","authenticated-orcid":true,"given":"Geoffrey W.","family":"Grime","sequence":"additional","affiliation":[{"name":"University of Surrey Ion Beam Centre , , ,","place":["Guildford, Surrey, U.K., GU2 7XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel M.","family":"Webb","sequence":"additional","affiliation":[{"name":"Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, MS69 , , ,","place":["Menlo Park, California, United States, 94025"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5792-3891","authenticated-orcid":true,"given":"Catia","family":"Costa","sequence":"additional","affiliation":[{"name":"University of Surrey Ion Beam Centre , , ,","place":["Guildford, Surrey, U.K., GU2 7XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Elizabeth","family":"Snell","sequence":"additional","affiliation":[{"name":"The University at Buffalo Hauptman-Woodward Institute , 700 Ellicott St. , , ,","place":["Buffalo, New York, United States, 14203"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0034-5167","authenticated-orcid":true,"given":"John F.","family":"Hunt","sequence":"additional","affiliation":[{"name":"Columbia University , , , ,","place":["New York, New York, United States, 10027"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0563-6468","authenticated-orcid":true,"given":"Liang","family":"Tong","sequence":"additional","affiliation":[{"name":"Columbia University , , , ,","place":["New York, New York, United States, 10027"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9440-3059","authenticated-orcid":true,"given":"Gaetano T.","family":"Montelione","sequence":"additional","affiliation":[{"name":"Rensselaer Polytechnic Institute , , , ,","place":["Troy, New York, United States, 12180"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Zigweid","sequence":"additional","affiliation":[{"name":"Seattle Structural Genomics Center for Infectious Diseases , , ,","place":["Seattle, Washington, United States, 98109-5219"]},{"name":"Seattle Children\u2019s Research Institute , , , ,","place":["Seattle, Washington, United States, 98101"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9570-5086","authenticated-orcid":true,"given":"Bart L.","family":"Staker","sequence":"additional","affiliation":[{"name":"Seattle Structural Genomics Center for Infectious Diseases , , ,","place":["Seattle, Washington, United States, 98109-5219"]},{"name":"Seattle Children\u2019s Research Institute , , , ,","place":["Seattle, Washington, United States, 98101"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J.","family":"Myler","sequence":"additional","affiliation":[{"name":"Seattle Structural Genomics Center for Infectious Diseases , , ,","place":["Seattle, Washington, United States, 98109-5219"]},{"name":"Seattle Children\u2019s Research Institute , , , ,","place":["Seattle, Washington, United States, 98101"]},{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8329-5665","authenticated-orcid":true,"given":"Elspeth F.","family":"Garman","sequence":"additional","affiliation":[{"name":"Dorothy Crowfoot Hodgkin Building, University of Oxford , , South Parks Road , ,","place":["Oxford, U.K., OX1 3QU"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,6,15]]},"reference":[{"issue":"1","key":"2026081008104693800_cit1","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1016\/j.cbpa.2010.11.004","article-title":"Metalloproteomics: forward and reverse approaches in\nmetalloprotein structural and functional characterization","volume":"15","author":"Shi","year":"2011","journal-title":"Curr. Opin. Chem. Biol."},{"issue":"7257","key":"2026081008104693800_cit2","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/nature08300","article-title":"Metalloproteins\nand metal sensing","volume":"460","author":"Waldron","year":"2009","journal-title":"Nature"},{"issue":"9","key":"2026081008104693800_cit3","doi-asserted-by":"publisher","first-page":"1765","DOI":"10.1016\/j.jinorgbio.2008.05.006","article-title":"Data mining\nof metal ion environments present in protein structures","volume":"102","author":"Zheng","year":"2008","journal-title":"J. Inorg. Biochem"},{"key":"2026081008104693800_cit4","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1021\/acs.chemrev.8b00201","article-title":"Targeting Metalloenzymes\nfor Therapeutic Intervention","volume":"119","author":"Chen","year":"2019","journal-title":"Chem. Rev."},{"issue":"1","key":"2026081008104693800_cit5","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1002\/1873-3468.14500","article-title":"Protein metalation\nin a nutshell","volume":"597","author":"Osman","year":"2023","journal-title":"FEBS Lett."},{"issue":"4123","key":"2026081008104693800_cit6","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1038\/162746a0","article-title":"Order of Stability\nof Metal Complexes","volume":"162","author":"Irving","year":"1948","journal-title":"Nature"},{"issue":"19","key":"2026081008104693800_cit7","doi-asserted-by":"publisher","first-page":"4446","DOI":"10.1021\/jp004602g","article-title":"Metal Selectivity in\nMetalloproteins: Zn2+ vs Mg2+","volume":"105","author":"Dudev","year":"2001","journal-title":"J. Phys. 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Biol."},{"issue":"5526","key":"2026081008104693800_cit10","doi-asserted-by":"publisher","first-page":"2488","DOI":"10.1126\/science.1060331","article-title":"Femtomolar\nsensitivity of metalloregulatory proteins\ncontrolling zinc homeostasis","volume":"292","author":"Outten","year":"2001","journal-title":"Science"},{"key":"2026081008104693800_cit11","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1146\/annurev.biochem.70.1.677","article-title":"Function, structure, and mechanism of intracellular\ncopper trafficking proteins","volume":"70","author":"Huffman","year":"2001","journal-title":"Annu. Rev. Biochem."},{"issue":"5415","key":"2026081008104693800_cit12","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1126\/science.284.5415.805","article-title":"Undetectable\nIntracellular Free Copper: The Requirement of a Copper Chaperone for\nSuperoxide Dismutase","volume":"284","author":"Rae","year":"1999","journal-title":"Science"},{"issue":"1","key":"2026081008104693800_cit13","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1042\/BJ20090422","article-title":"Copper(I)-mediated protein-protein interactions result\nfrom suboptimal interaction surfaces","volume":"422","author":"Banci","year":"2009","journal-title":"Biochem.\nJ."},{"issue":"1","key":"2026081008104693800_cit14","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/nrmicro2057","article-title":"How do bacterial cells ensure that metalloproteins\nget the correct metal?","volume":"7","author":"Waldron","year":"2009","journal-title":"Nat. Rev. Microbiol"},{"issue":"2","key":"2026081008104693800_cit15","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.pbiomolbio.2004.09.005","article-title":"Elemental analysis of proteins by microPIXE","volume":"89","author":"Garman","year":"2005","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"2026081008104693800_cit16","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/j.nimb.2023.03.025","article-title":"The identification\nand quantification of metal atoms\nin proteins using microPIXE: A critical evaluation","volume":"540","author":"Grime","year":"2023","journal-title":"Nucl. Instrum. Methods Phys. Res., Sect. B"},{"issue":"1","key":"2026081008104693800_cit17","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1021\/jacs.9b09186","article-title":"High-Throughput\nPIXE as an Essential Quantitative Assay for Accurate Metalloprotein\nStructural Analysis: Development and Application","volume":"142","author":"Grime","year":"2020","journal-title":"J. Am. Chem. Soc."},{"issue":"3\u20134","key":"2026081008104693800_cit18","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/S0162-0134(00)00086-6","article-title":"Mutational and spectroscopic studies of the significance\nof the active site glutamine to metal ion specificity in superoxide\ndismutase","volume":"80","author":"Schwartz","year":"2000","journal-title":"J. Inorg. Biochem."},{"issue":"10","key":"2026081008104693800_cit19","doi-asserted-by":"publisher","first-page":"3534","DOI":"10.1073\/pnas.0408029102","article-title":"Long-range electron transfer","volume":"102","author":"Gray","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"1","key":"2026081008104693800_cit20","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1021\/cr050241v","article-title":"Cytochrome c: Occurrence and Functions","volume":"106","author":"Bertini","year":"2006","journal-title":"Chem. Rev."},{"issue":"6685","key":"2026081008104693800_cit21","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/31159","article-title":"Deciphering the biology\nof Mycobacterium tuberculosis from\nthe complete genome sequence","volume":"393","author":"Cole","year":"1998","journal-title":"Nature"},{"issue":"13","key":"2026081008104693800_cit22","doi-asserted-by":"publisher","first-page":"9914","DOI":"10.1074\/jbc.M609974200","article-title":"Crystal structure and function of the zinc uptake regulator FurB\nfrom Mycobacterium tuberculosis","volume":"282","author":"Lucarelli","year":"2007","journal-title":"J. Biol. Chem."},{"key":"2026081008104693800_cit23","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.abb.2014.01.029","article-title":"The FUR\n(ferric uptake regulator) superfamily: diversity and versatility of\nkey transcriptional regulators","volume":"546","author":"Fillat","year":"2014","journal-title":"Arch. Biochem.\nBiophys."},{"issue":"3","key":"2026081008104693800_cit24","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1016\/S1074-5521(02)00112-6","article-title":"MgF(3)(\u2212)\nas a transition state analog of phosphoryl transfer","volume":"9","author":"Graham","year":"2002","journal-title":"Chem. Biol."},{"issue":"5","key":"2026081008104693800_cit25","doi-asserted-by":"publisher","first-page":"493","DOI":"10.2174\/187152609789105687","article-title":"The Seattle Structural\nGenomics Center\nfor Infectious Disease (SSGCID)","volume":"9","author":"Myler","year":"2009","journal-title":"Infect. Disord.:Drug\nTargets"},{"key":"2026081008104693800_cit26","unstructured":"Kramer Green, R.\n          \n          RCSB\nScientific Support & Customer Service Lead. 2025."},{"issue":"Pt 4","key":"2026081008104693800_cit27","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1107\/S0907444911054515","article-title":"PDB_REDO: constructive\nvalidation, more than just looking for errors","volume":"68","author":"Joosten","year":"2012","journal-title":"Acta Crystallogr., Sect. D:Biol. Crystallogr."},{"issue":"Pt 4","key":"2026081008104693800_cit28","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1107\/S2052252514009324","article-title":"The PDB_REDO server\nfor macromolecular structure model optimization","volume":"1","author":"Joosten","year":"2014","journal-title":"IUCrJ"},{"key":"2026081008104693800_cit29","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1107\/S2059798323003595","article-title":"The CCP4 suite: integrative software for macromolecular\ncrystallography","volume":"79","author":"Agirre","year":"2023","journal-title":"Acta Crystallogr., Sect. D:\nBiol. Crystallogr."},{"issue":"Pt 4","key":"2026081008104693800_cit30","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1107\/S0907444911035918","article-title":"Statistical\nquality indicators for electron-density maps","volume":"68","author":"Tickle","year":"2012","journal-title":"Acta Crystallogr., Sect. D Biol. Crystallogr."},{"key":"2026081008104693800_cit31","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1107\/S0907444911007281","article-title":"Presenting your\nstructures: the CCP4mg molecular-graphics software","volume":"67","author":"McNicholas","year":"2011","journal-title":"Acta Crystallogr., Sect. D Biol. Crystallogr."},{"issue":"2","key":"2026081008104693800_cit32","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1007\/BF00203823","article-title":"High-level production\nof uniformly (1)(5)N- and (1)(3)C-enriched\nfusion proteins in Escherichia coli","volume":"7","author":"Jansson","year":"1996","journal-title":"J. Biomol. NMR"},{"issue":"1","key":"2026081008104693800_cit33","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/j.jsb.2010.07.011","article-title":"The high-throughput protein sample production\nplatform of the Northeast Structural Genomics Consortium","volume":"172","author":"Xiao","year":"2010","journal-title":"J. Struct. Biol."},{"key":"2026081008104693800_cit34","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/B978-0-12-381274-2.00002-9","article-title":"Preparation\nof Protein Samples for NMR Structure, Function, and Small-Molecule\nScreening Studies","volume-title":"Methods in Enzymology","author":"Acton","year":"2011"},{"issue":"Pt 9","key":"2026081008104693800_cit35","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1107\/S1744309111018367","article-title":"High-throughput\nprotein production and purification at the Seattle Structural Genomics\nCenter for Infectious Disease","volume":"67","author":"Bryan","year":"2011","journal-title":"Acta Crystallogr.,\nSect. F:Struct. Biol. Cryst. Commun."},{"key":"2026081008104693800_cit36","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1016\/j.nimb.2004.01.091","article-title":"The new Surrey ion beam analysis\nfacility","volume":"219-220","author":"Simon","year":"2004","journal-title":"Nucl. Instrum. Methods Phys. Res.,\nSect. B"},{"key":"2026081008104693800_cit37","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/0168-583X(91)95490-5","article-title":"The Oxford\nsubmicron nuclear microscopy facility","volume":"54","author":"Grime","year":"1991","journal-title":"Nucl.\nInstrum. Methods Phys. Res., Sect. B"},{"key":"2026081008104693800_cit38","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1063\/1.3625338","article-title":"The MicroAnalysis\nToolkit:\nX-ray Fluorescence Image Processing Software","volume":"1365","author":"Webb","year":"2011","journal-title":"AIP Conf. Proc."},{"issue":"1","key":"2026081008104693800_cit39","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/j.sab.2006.12.002","article-title":"A multiplatform\ncode for the analysis of energy-dispersive X-ray fluorescence spectra","volume":"62","author":"Sole\u0301","year":"2007","journal-title":"Spectrochim. Acta, Part B"},{"issue":"3","key":"2026081008104693800_cit40","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1016\/j.bmc.2016.11.013","article-title":"Rickettsia prowazekii methionine aminopeptidase\nas a promising target for the development of antibacterial agents","volume":"25","author":"Helgren","year":"2017","journal-title":"Bioorg. Med. Chem."},{"issue":"25","key":"2026081008104693800_cit41","doi-asserted-by":"publisher","first-page":"7776","DOI":"10.1021\/ja068168t","article-title":"Which one\namong Zn(II), Co(II), Mn(II),\nand Fe(II) is the most efficient ion for the methionine aminopeptidase\ncatalyzed reaction?","volume":"129","author":"Leopoldini","year":"2007","journal-title":"J. Am. Chem. Soc."},{"issue":"34","key":"2026081008104693800_cit42","doi-asserted-by":"publisher","first-page":"11079","DOI":"10.1021\/bi990872h","article-title":"The methionyl\naminopeptidase from Escherichia coli can function as an iron(II) enzyme","volume":"38","author":"D\u2019souz","year":"1999","journal-title":"Biochemistry"},{"key":"2026081008104693800_cit43","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1107\/S0907444911001314","article-title":"REFMAC5\nfor the refinement of macromolecular crystal structures","volume":"67","author":"Murshudov","year":"2011","journal-title":"Acta Crystallogr., Sect. D:Biol. Crystallogr."},{"key":"2026081008104693800_cit44","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1107\/S2052252520003917","article-title":"A structural\nstudy of TatD from Staphylococcus aureus elucidates a putative DNA-binding\nmode of a Mg(2+)-dependent nuclease","volume":"7","author":"Lee","year":"2020","journal-title":"IUCrJ"},{"issue":"40","key":"2026081008104693800_cit45","doi-asserted-by":"publisher","first-page":"5841","DOI":"10.1021\/acs.biochem.8b00713","article-title":"Structure\nand Reaction Mechanism\nof the LigJ. Hydratase: An Enzyme Critical for the Bacterial Degradation\nof Lignin in the Protocatechuate 4,5-Cleavage Pathway","volume":"57","author":"Hogancamp","year":"2018","journal-title":"Biochemistry"},{"issue":"5","key":"2026081008104693800_cit46","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/nchembio.1229","article-title":"Two\nFe-S clusters catalyze\nsulfur insertion by radical-SAM methylthiotransferases","volume":"9","author":"Forouhar","year":"2013","journal-title":"Nat. Chem. Biol."},{"issue":"2","key":"2026081008104693800_cit47","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1107\/S1600577515002349","article-title":"Indications\nof radiation\ndamage in ferredoxin microcrystals using high-intensity X-FEL beams","volume":"22","author":"Nass","year":"2015","journal-title":"J. Synchrotron Radiat."},{"issue":"8","key":"2026081008104693800_cit48","doi-asserted-by":"publisher","first-page":"5792","DOI":"10.1074\/jbc.M109.065516","article-title":"Post-translational modification of ribosomal proteins:\nstructural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine\nmethylthiotransferase","volume":"285","author":"Arragain","year":"2010","journal-title":"J. Biol. 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