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wwPDBX-rayStructureValidationSummaryReportiOMay26,202004:40pmBSTPDBID:1E15Title:ChitinaseBfromSerratiaMarcescensAuthors:VanAalten,D.
M.
F.
;Synstad,B.
;Brurberg,M.
B.
;Hough,E.
;Riise,B.
W.
;Eijsink,V.
G.
H.
;Wierenga,R.
K.
Depositedon:2000-04-18Resolution:1.
90(reported)ThisisawwPDBX-rayStructureValidationSummaryReportforapubliclyreleasedPDBentry.
Wewelcomeyourcommentsatvalidation@mail.
wwpdb.
orgAuserguideisavailableathttps://www.
wwpdb.
org/validation/2017/XrayValidationReportHelpwithspecichelpavailableeverywhereyouseetheiOsymbol.
Thefollowingversionsofsoftwareanddata(seereferencesiO)wereusedintheproductionofthisreport:MolProbity:4.
02b-467Xtriage(Phenix):NOTEXECUTEDEDS:NOTEXECUTEDPercentilestatistics:20191225.
v01(usingentriesinthePDBarchiveDecember25th2019)Idealgeometry(proteins):Engh&Huber(2001)Idealgeometry(DNA,RNA):Parkinsonetal.
(1996)ValidationPipeline(wwPDB-VP):2.
11Page2wwPDBX-rayStructureValidationSummaryReport1E151OverallqualityataglanceiOThefollowingexperimentaltechniqueswereusedtodeterminethestructure:X-RAYDIFFRACTIONThereportedresolutionofthisentryis1.
90.
Percentilescores(rangingbetween0-100)forglobalvalidationmetricsoftheentryareshowninthefollowinggraphic.
Thetableshowsthenumberofentriesonwhichthescoresarebased.
MetricWholearchive(#Entries)Similarresolution(#Entries,resolutionrange())Clashscore1416146847(1.
90-1.
90)Ramachandranoutliers1389816760(1.
90-1.
90)Sidechainoutliers1389456760(1.
90-1.
90)Thetablebelowsummarisesthegeometricissuesobservedacrossthepolymericchainsandtheirttotheelectrondensity.
Thered,orange,yellowandgreensegmentsonthelowerbarindicatethefractionofresiduesthatcontainoutliersfor>=3,2,1and0typesofgeometricqualitycriteriarespectively.
Agreysegmentrepresentsthefractionofresiduesthatarenotmodelled.
Thenumericvalueforeachfractionisindicatedbelowthecorrespondingsegment,withadotrepresentingfractionsI450V457T460A466Y473Q476K494R497V498A499Page5wwPDBX-rayStructureValidationSummaryReport1E154DataandrenementstatisticsiOXtriage(Phenix)andEDSwerenotexecuted-thissectionisthereforeincomplete.
PropertyValueSourceSpacegroupP212121DepositorCellconstantsa,b,c,α,β,γ56.
13106.
59187.
3390.
0090.
0090.
00DepositorResolution()38.
871.
90Depositor%Datacompleteness(inresolutionrange)99.
4(38.
87-1.
90)DepositorRmerge0.
09DepositorRsym(Notavailable)DepositorRenementprogramCNS1.
0DepositorR,Rfree0.
183,0.
212DepositorEstimatedtwinningfractionNotwinningtoreport.
XtriageTotalnumberofatoms8062wwPDB-VPAverageB,allatoms(2)25.
0wwPDB-VPPage6wwPDBX-rayStructureValidationSummaryReport1E155ModelqualityiO5.
1StandardgeometryiOTheZscoreforabondlength(orangle)isthenumberofstandarddeviationstheobservedvalueisremovedfromtheexpectedvalue.
Abondlength(orangle)with|Z|>5isconsideredanoutlierworthinspection.
RMSZistheroot-mean-squareofallZscoresofthebondlengths(orangles).
MolChainBondlengthsBondanglesRMSZ#|Z|>5RMSZ#|Z|>51A0.
750/40130.
823/5470(0.
1%)1B0.
770/40120.
884/5467(0.
1%)AllAll0.
760/80250.
857/10937(0.
1%)Therearenobondlengthoutliers.
Theworst5of7bondangleoutliersarelistedbelow:MolChainResTypeAtomsZObserved(o)Ideal(o)1B316ASPC-N-CD-19.
8276.
99120.
601B316ASPC-N-CA13.
52178.
78122.
001B323TYRN-CA-C-9.
1986.
19111.
001A323TYRN-CA-C-7.
5790.
56111.
001B317PROCA-N-CD-6.
49102.
41111.
50Therearenochiralityoutliers.
Therearenoplanarityoutliers.
5.
2Too-closecontactsiOInthefollowingtable,theNon-HandH(model)columnslistthenumberofnon-hydrogenatomsandhydrogenatomsinthechainrespectively.
TheH(added)columnliststhenumberofhydrogenatomsaddedandoptimizedbyMolProbity.
TheClashescolumnliststhenumberofclasheswithintheasymmetricunit,whereasSymm-Clasheslistssymmetryrelatedclashes.
MolChainNon-HH(model)H(added)ClashesSymm-Clashes1A3902037365301B3901037346102A13000202B1290010AllAll8062074701130Page7wwPDBX-rayStructureValidationSummaryReport1E15Theall-atomclashscoreisdenedasthenumberofclashesfoundper1000atoms(includinghydrogenatoms).
Theall-atomclashscoreforthisstructureis7.
Theworst5of113closecontactswithinthesameasymmetricunitarelistedbelow,sortedbytheirclashmagnitude.
Atom-1Atom-2Interatomicdistance()Clashoverlap()1:A:222:LYS:HD31:A:222:LYS:N1.
621.
091:A:222:LYS:CD1:A:222:LYS:H1.
651.
081:B:345:LEU:HA1:B:348:MET:HE31.
361.
061:A:319:PRO:O1:A:321:THR:N1.
931.
011:A:222:LYS:H1:A:222:LYS:HD30.
860.
99Therearenosymmetry-relatedclashes.
5.
3TorsionanglesiO5.
3.
1ProteinbackboneiOInthefollowingtable,thePercentilescolumnshowsthepercentRamachandranoutliersofthechainasapercentilescorewithrespecttoallX-rayentriesfollowedbythatwithrespecttoentriesofsimilarresolution.
TheAnalysedcolumnshowsthenumberofresiduesforwhichthebackboneconformationwasanalysed,andthetotalnumberofresidues.
MolChainAnalysedFavouredAllowedOutliersPercentiles1A494/499(99%)478(97%)14(3%)2(0%)34241B494/499(99%)479(97%)9(2%)6(1%)134AllAll988/998(99%)957(97%)23(2%)8(1%)1995of8Ramachandranoutliersarelistedbelow:MolChainResType1A320SER1A322ASP1B148ALA1B317PRO1B320SERPage8wwPDBX-rayStructureValidationSummaryReport1E155.
3.
2ProteinsidechainsiOInthefollowingtable,thePercentilescolumnshowsthepercentsidechainoutliersofthechainasapercentilescorewithrespecttoallX-rayentriesfollowedbythatwithrespecttoentriesofsimilarresolution.
TheAnalysedcolumnshowsthenumberofresiduesforwhichthesidechainconformationwasanalysed,andthetotalnumberofresidues.
MolChainAnalysedRotamericOutliersPercentiles1A403/405(100%)393(98%)10(2%)47411B402/405(99%)392(98%)10(2%)4741AllAll805/810(99%)785(98%)20(2%)47415of20residueswithanon-rotamericsidechainarelistedbelow:MolChainResType1A447ASN1B222LYS1B378THR1A378THR1A380ASPSomesidechainscanbeippedtoimprovehydrogenbondingandreduceclashes.
5of24suchsidechainsarelistedbelow:MolChainResType1A447ASN1B180GLN1B394GLN1B112ASN1B147GLN5.
3.
3RNAiOTherearenoRNAmoleculesinthisentry.
5.
4Non-standardresiduesinprotein,DNA,RNAchainsiOTherearenonon-standardprotein/DNA/RNAresiduesinthisentry.
Page9wwPDBX-rayStructureValidationSummaryReport1E155.
5CarbohydratesiOTherearenocarbohydratesinthisentry.
5.
6LigandgeometryiOTherearenoligandsinthisentry.
5.
7OtherpolymersiOTherearenosuchresiduesinthisentry.
5.
8PolymerlinkageissuesiOTherearenochainbreaksinthisentry.
Page10wwPDBX-rayStructureValidationSummaryReport1E156FitofmodelanddataiO6.
1Protein,DNAandRNAchainsiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
2Non-standardresiduesinprotein,DNA,RNAchainsiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
3CarbohydratesiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
4LigandsiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
5OtherpolymersiOEDSwasnotexecuted-thissectionisthereforeempty.
M.
F.
;Synstad,B.
;Brurberg,M.
B.
;Hough,E.
;Riise,B.
W.
;Eijsink,V.
G.
H.
;Wierenga,R.
K.
Depositedon:2000-04-18Resolution:1.
90(reported)ThisisawwPDBX-rayStructureValidationSummaryReportforapubliclyreleasedPDBentry.
Wewelcomeyourcommentsatvalidation@mail.
wwpdb.
orgAuserguideisavailableathttps://www.
wwpdb.
org/validation/2017/XrayValidationReportHelpwithspecichelpavailableeverywhereyouseetheiOsymbol.
Thefollowingversionsofsoftwareanddata(seereferencesiO)wereusedintheproductionofthisreport:MolProbity:4.
02b-467Xtriage(Phenix):NOTEXECUTEDEDS:NOTEXECUTEDPercentilestatistics:20191225.
v01(usingentriesinthePDBarchiveDecember25th2019)Idealgeometry(proteins):Engh&Huber(2001)Idealgeometry(DNA,RNA):Parkinsonetal.
(1996)ValidationPipeline(wwPDB-VP):2.
11Page2wwPDBX-rayStructureValidationSummaryReport1E151OverallqualityataglanceiOThefollowingexperimentaltechniqueswereusedtodeterminethestructure:X-RAYDIFFRACTIONThereportedresolutionofthisentryis1.
90.
Percentilescores(rangingbetween0-100)forglobalvalidationmetricsoftheentryareshowninthefollowinggraphic.
Thetableshowsthenumberofentriesonwhichthescoresarebased.
MetricWholearchive(#Entries)Similarresolution(#Entries,resolutionrange())Clashscore1416146847(1.
90-1.
90)Ramachandranoutliers1389816760(1.
90-1.
90)Sidechainoutliers1389456760(1.
90-1.
90)Thetablebelowsummarisesthegeometricissuesobservedacrossthepolymericchainsandtheirttotheelectrondensity.
Thered,orange,yellowandgreensegmentsonthelowerbarindicatethefractionofresiduesthatcontainoutliersfor>=3,2,1and0typesofgeometricqualitycriteriarespectively.
Agreysegmentrepresentsthefractionofresiduesthatarenotmodelled.
Thenumericvalueforeachfractionisindicatedbelowthecorrespondingsegment,withadotrepresentingfractionsI450V457T460A466Y473Q476K494R497V498A499Page5wwPDBX-rayStructureValidationSummaryReport1E154DataandrenementstatisticsiOXtriage(Phenix)andEDSwerenotexecuted-thissectionisthereforeincomplete.
PropertyValueSourceSpacegroupP212121DepositorCellconstantsa,b,c,α,β,γ56.
13106.
59187.
3390.
0090.
0090.
00DepositorResolution()38.
871.
90Depositor%Datacompleteness(inresolutionrange)99.
4(38.
87-1.
90)DepositorRmerge0.
09DepositorRsym(Notavailable)DepositorRenementprogramCNS1.
0DepositorR,Rfree0.
183,0.
212DepositorEstimatedtwinningfractionNotwinningtoreport.
XtriageTotalnumberofatoms8062wwPDB-VPAverageB,allatoms(2)25.
0wwPDB-VPPage6wwPDBX-rayStructureValidationSummaryReport1E155ModelqualityiO5.
1StandardgeometryiOTheZscoreforabondlength(orangle)isthenumberofstandarddeviationstheobservedvalueisremovedfromtheexpectedvalue.
Abondlength(orangle)with|Z|>5isconsideredanoutlierworthinspection.
RMSZistheroot-mean-squareofallZscoresofthebondlengths(orangles).
MolChainBondlengthsBondanglesRMSZ#|Z|>5RMSZ#|Z|>51A0.
750/40130.
823/5470(0.
1%)1B0.
770/40120.
884/5467(0.
1%)AllAll0.
760/80250.
857/10937(0.
1%)Therearenobondlengthoutliers.
Theworst5of7bondangleoutliersarelistedbelow:MolChainResTypeAtomsZObserved(o)Ideal(o)1B316ASPC-N-CD-19.
8276.
99120.
601B316ASPC-N-CA13.
52178.
78122.
001B323TYRN-CA-C-9.
1986.
19111.
001A323TYRN-CA-C-7.
5790.
56111.
001B317PROCA-N-CD-6.
49102.
41111.
50Therearenochiralityoutliers.
Therearenoplanarityoutliers.
5.
2Too-closecontactsiOInthefollowingtable,theNon-HandH(model)columnslistthenumberofnon-hydrogenatomsandhydrogenatomsinthechainrespectively.
TheH(added)columnliststhenumberofhydrogenatomsaddedandoptimizedbyMolProbity.
TheClashescolumnliststhenumberofclasheswithintheasymmetricunit,whereasSymm-Clasheslistssymmetryrelatedclashes.
MolChainNon-HH(model)H(added)ClashesSymm-Clashes1A3902037365301B3901037346102A13000202B1290010AllAll8062074701130Page7wwPDBX-rayStructureValidationSummaryReport1E15Theall-atomclashscoreisdenedasthenumberofclashesfoundper1000atoms(includinghydrogenatoms).
Theall-atomclashscoreforthisstructureis7.
Theworst5of113closecontactswithinthesameasymmetricunitarelistedbelow,sortedbytheirclashmagnitude.
Atom-1Atom-2Interatomicdistance()Clashoverlap()1:A:222:LYS:HD31:A:222:LYS:N1.
621.
091:A:222:LYS:CD1:A:222:LYS:H1.
651.
081:B:345:LEU:HA1:B:348:MET:HE31.
361.
061:A:319:PRO:O1:A:321:THR:N1.
931.
011:A:222:LYS:H1:A:222:LYS:HD30.
860.
99Therearenosymmetry-relatedclashes.
5.
3TorsionanglesiO5.
3.
1ProteinbackboneiOInthefollowingtable,thePercentilescolumnshowsthepercentRamachandranoutliersofthechainasapercentilescorewithrespecttoallX-rayentriesfollowedbythatwithrespecttoentriesofsimilarresolution.
TheAnalysedcolumnshowsthenumberofresiduesforwhichthebackboneconformationwasanalysed,andthetotalnumberofresidues.
MolChainAnalysedFavouredAllowedOutliersPercentiles1A494/499(99%)478(97%)14(3%)2(0%)34241B494/499(99%)479(97%)9(2%)6(1%)134AllAll988/998(99%)957(97%)23(2%)8(1%)1995of8Ramachandranoutliersarelistedbelow:MolChainResType1A320SER1A322ASP1B148ALA1B317PRO1B320SERPage8wwPDBX-rayStructureValidationSummaryReport1E155.
3.
2ProteinsidechainsiOInthefollowingtable,thePercentilescolumnshowsthepercentsidechainoutliersofthechainasapercentilescorewithrespecttoallX-rayentriesfollowedbythatwithrespecttoentriesofsimilarresolution.
TheAnalysedcolumnshowsthenumberofresiduesforwhichthesidechainconformationwasanalysed,andthetotalnumberofresidues.
MolChainAnalysedRotamericOutliersPercentiles1A403/405(100%)393(98%)10(2%)47411B402/405(99%)392(98%)10(2%)4741AllAll805/810(99%)785(98%)20(2%)47415of20residueswithanon-rotamericsidechainarelistedbelow:MolChainResType1A447ASN1B222LYS1B378THR1A378THR1A380ASPSomesidechainscanbeippedtoimprovehydrogenbondingandreduceclashes.
5of24suchsidechainsarelistedbelow:MolChainResType1A447ASN1B180GLN1B394GLN1B112ASN1B147GLN5.
3.
3RNAiOTherearenoRNAmoleculesinthisentry.
5.
4Non-standardresiduesinprotein,DNA,RNAchainsiOTherearenonon-standardprotein/DNA/RNAresiduesinthisentry.
Page9wwPDBX-rayStructureValidationSummaryReport1E155.
5CarbohydratesiOTherearenocarbohydratesinthisentry.
5.
6LigandgeometryiOTherearenoligandsinthisentry.
5.
7OtherpolymersiOTherearenosuchresiduesinthisentry.
5.
8PolymerlinkageissuesiOTherearenochainbreaksinthisentry.
Page10wwPDBX-rayStructureValidationSummaryReport1E156FitofmodelanddataiO6.
1Protein,DNAandRNAchainsiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
2Non-standardresiduesinprotein,DNA,RNAchainsiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
3CarbohydratesiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
4LigandsiOEDSwasnotexecuted-thissectionisthereforeempty.
6.
5OtherpolymersiOEDSwasnotexecuted-thissectionisthereforeempty.
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