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Macromolecular crystallography was preceded by the older field of small-molecule [[x-ray crystallography]] (for structures with less than a few hundred atoms). Small-molecule [[diffraction]] data extends to much higher [[Resolution (electron density)|resolution]] than feasible for macromolecules, and has a very clean mathematical relationship between the data and the atomic model. The residual, or R-factor, measures the agreement between the experimental data and the values back-calculated from the atomic model. For a well-determined small-molecule structure the R-factor is nearly as small as the uncertainty in the experimental data (well under 5%). Therefore, that one test by itself provides most of the validation needed, but a number of additional consistency and methodology checks are done by automated software<ref>{{Cite journal | vauthors = Spek AL |year=2003 |title=Single-crystal structure validation with the program PLATON |journal=Journal of Applied Crystallography |volume= 36 |issue=1 |pages=7–13 |doi=10.1107/S0021889802022112|bibcode=2003JApCr..36....7S |doi-access=free }}</ref> as a requirement for small-molecule crystal structure papers submitted to the [[International Union of Crystallography]] (IUCr) journals such as [[Acta Crystallographica]] section B or C. Atomic coordinates of these small-molecule structures are archived and accessed through the [[Cambridge Structural Database]] (CSD)<ref>{{cite journal | vauthors = Allen FH | title = The Cambridge Structural Database: a quarter of a million crystal structures and rising | journal = Acta Crystallographica Section B | volume = 58 | issue = Pt 3 Pt 1 | pages = 380–8 | date = June 2002 | pmid = 12037359 | doi = 10.1107/S0108768102003890 | bibcode = 2002AcCrB..58..380A | doi-access = }}</ref> or the [[Crystallography Open Database]] (COD).<ref>{{cite journal | vauthors = Gražulis S, Chateigner D, Downs RT, Yokochi AF, Quirós M, Lutterotti L, Manakova E, Butkus J, Moeck P, Le Bail A | display-authors = 6 | title = Crystallography Open Database - an open-access collection of crystal structures | journal = Journal of Applied Crystallography | volume = 42 | issue = Pt 4 | pages = 726–729 | date = August 2009 | pmid = 22477773 | pmc = 3253730 | doi = 10.1107/s0021889809016690 | bibcode = 2009JApCr..42..726G }}</ref>
The first macromolecular validation software was developed around 1990, for proteins. It included Rfree [[cross-validation (statistics)|cross-validation]] for model-to-data match,<ref name="Rfree">{{cite journal | vauthors = Brünger AT | title = Free R value: a novel statistical quantity for assessing the accuracy of crystal structures | journal = Nature | volume = 355 | issue = 6359 | pages = 472–5 | date = January 1992 | pmid = 18481394 | doi = 10.1038/355472a0 | author-link = Axel T. Brunger | bibcode = 1992Natur.355..472B | s2cid = 2462215 }}</ref> bond length and angle parameters for covalent geometry,<ref name="Engh">{{cite journal |vauthors=Engh RA, Huber R |year=1991 |title=Accurate bond and angle parameters for X-ray protein structure refinement |journal=Acta Crystallographica Section A |volume=47 |issue=4 |pages=392–400|doi=10.1107/s0108767391001071 |bibcode=1991AcCrA..47..392E }}</ref> and sidechain and backbone conformational criteria.<ref name="Ponder&Richards">{{cite journal |vauthors=Ponder JW, Richards FM |year=1987 |title=Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes |journal=Journal of Molecular Biology |volume=193 |issue=4 |pages=775–791 |doi=10.1016/0022-2836(87)90358-5|pmid=2441069 }}</ref><ref name="procheck">{{cite journal |vauthors=Laskowski RA, MacArthur MW, Moss DS, Thornton JM |author4-link=Janet Thornton |year=1993 |title=PROCHECK: a program to check the stereochemical quality of protein structures |journal=Journal of Applied Crystallography |volume=26 |issue=2 |pages=283–291 |doi=10.1107/s0021889892009944|bibcode=1993JApCr..26..283L }}</ref><ref name="whatif">{{cite journal | vauthors = Hooft RW, Vriend G, Sander C, Abola EE | title = Errors in protein structures | journal = Nature | volume = 381 | issue = 6580 | pages = 272 | date = May 1996 | pmid = 8692262 | doi = 10.1038/381272a0 | bibcode = 1996Natur.381..272H | s2cid = 4368507 | doi-access = free }}</ref> For macromolecular structures, the atomic models are deposited in the [[Protein Data Bank]] (PDB), still the single archive of this data. The PDB was established in the 1970s at [[Brookhaven National Laboratory]],<ref>{{cite journal | vauthors = Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M | display-authors = 6 | title = The Protein Data Bank: a computer-based archival file for macromolecular structures | journal = Journal of Molecular Biology | volume = 112 | issue = 3 | pages = 535–42 | date = May 1977 | pmid = 875032 | doi = 10.1016/s0022-2836(77)80200-3 | author7-link = Olga Kennard }}</ref> moved in 2000 to the [http://www.rcsb.org/pdb RCSB] (Research Collaboration for Structural Biology) centered at [[Rutgers]],<ref>{{cite journal | vauthors = Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE | display-authors = 6 | title = The Protein Data Bank | journal = Nucleic Acids Research | volume = 28 | issue = 1 | pages = 235–42 | date = January 2000 | pmid = 10592235 | pmc = 102472 | doi = 10.1093/nar/28.1.235 | author8-link = Philip Bourne | author-link = Helen M. Berman }}</ref> and expanded in 2003 to become the [http://www.wwpdb.org/ wwPDB] (worldwide Protein Data Bank),<ref name="wwPDB">{{cite journal | vauthors = Berman H, Henrick K, Nakamura H | title = Announcing the worldwide Protein Data Bank | journal = Nature Structural Biology | volume = 10 | issue = 12 | pages = 980 | date = December 2003 | pmid = 14634627 | doi = 10.1038/nsb1203-980 | s2cid = 2616817 | author-link = Helen M. Berman | doi-access = free }}</ref> with access sites added in Europe ([http://pdbe.org|PDBe]) and Asia ([http://www.pdbj.org|PDBj]), and with NMR data handled at the [http://www.bmrb.wisc.edu BioMagResBank (BMRB)] in Wisconsin.
Validation rapidly became standard in the field,<ref name="Kleywegt2000">{{cite journal | vauthors = Kleywegt GJ |year= 2000 |title= Validation of protein crystal structures |journal=Acta Crystallographica Section D |volume=56 |issue= Pt 3 |pages=18–19|doi= 10.1107/s0907444999016364 |pmid= 10713511 |bibcode= 2000AcCrD..56..249K }}</ref> with further developments described below. *Obviously needs expansion*
A large boost was given to the applicability of comprehensive validation for both x-ray and NMR as of February 1, 2008, when the worldwide [[Protein Data Bank]] (wwPDB) made mandatory the deposition of experimental data along with atomic coordinates. Since 2012 strong forms of validation have been in the process of being adopted for [http://www.wwpdb.org/validation.html wwPDB deposition] from recommendations of the wwPDB Validation Task Force committees for [[x-ray crystallography]],<ref name="xrayVTF">{{cite journal | vauthors = Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH | display-authors = 6 | title = A new generation of crystallographic validation tools for the protein data bank | journal = Structure | volume = 19 | issue = 10 | pages = 1395–412 | date = October 2011 | pmid = 22000512 | pmc = 3195755 | doi = 10.1016/j.str.2011.08.006 | author12-link = Jane Richardson (chemist) | author7-link = Gerard Kleywegt | author4-link = Axel Brunger }}</ref> for NMR,<ref name="nmrVTF">{{cite journal | vauthors = Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL | display-authors = 6 | title = Recommendations of the wwPDB NMR Validation Task Force | journal = Structure | volume = 21 | issue = 9 | pages = 1563–70 | date = September 2013 | pmid = 24010715 | pmc = 3884077 | doi = 10.1016/j.str.2013.07.021 | author12-link = Gerard Kleywegt | author11-link = Helen M. Berman | author3-link = Ad Bax | author6-link = Jane Richardson (chemist) }}</ref> for SAXS ([[SAXS|small-angle x-ray scattering]]), and for cryoEM (cryo-[[Electron Microscopy]]).<ref name="emVTF">{{cite journal | vauthors = Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL | display-authors = 6 | title = Outcome of the first electron microscopy validation task force meeting | journal = Structure | volume = 20 | issue = 2 | pages = 205–14 | date = February 2012 | pmid = 22325770 | pmc = 3328769 | doi = 10.1016/j.str.2011.12.014 | author16-link = Michael Rossmann | author-link = Richard Henderson (biologist) }}</ref>
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Geometry-based validation tools similar to those used in X-ray crystallography can be used to highlight implausible modeling choices and guide modeler toward more native-like structures. The CaBLAM method, which only uses Cα atoms,<ref>{{cite web |title=CaBLAM Validation in Phenix |url=https://phenix-online.org/documentation/reference/cablam_validation.html |website=phenix-online.org}}</ref> is suitable for low-resolution structures from cyro-EM.<ref>{{cite journal |last1=Rohou |first1=Alexis |title=Improving cryo-EM structure validation |journal=Nature Methods |date=February 2021 |volume=18 |issue=2 |pages=130–131 |doi=10.1038/s41592-021-01062-1|pmid=33542515 |s2cid=231820981 }}</ref>
A way to compute the [[difference density map]] has been formulated for cyro-EM.<ref>{{cite journal |last1=Yamashita |first1=Keitaro |last2=Palmer |first2=Colin M. |last3=Burnley |first3=Tom |last4=Murshudov |first4=Garib N. |title=Cryo-EM single-particle structure refinement and map calculation using Servalcat |journal=Acta Crystallographica Section D
== In SAXS ==
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** [http://emdatabank.org/deposit.html EM Data Bank, for EM map deposition]
** [http://www.wwpdb.org/em/ EMDB at the PDB, info on ftp download of maps]
** [https://cci.lbl.gov/ceres CERES], rebuilds (and hopefully improves) Cyro-EM models using the latest version of PHENIX<ref>{{cite journal |last1=Liebschner |first1=D |last2=Afonine |first2=PV |last3=Moriarty |first3=NW |last4=Poon |first4=BK |last5=Chen |first5=VB |last6=Adams |first6=PD |title=CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. |journal=Acta Crystallographica
=== Link references ===
{{reflist}}
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