6ORD

Crystal structure of tRNA^ Ala(GGC) U32-A38 bound to cognate 70S A site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Disruption of evolutionarily correlated tRNA elements impairs accurate decoding

Nguyen, H.A.Sunita, S.Dunham, C.M.

(2020) Proc Natl Acad Sci U S A 


Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
QB, XB
256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
QC, XC
239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
QD, XD
209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
QE, XE
162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
QF, XF
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
QG, XG
156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
QH, XH
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
QI, XI
128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
QJ, XJ
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
QK, XK
129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
QL, XL
132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
QM, XM
126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
QN, XN
61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
QO, XO
89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
QP, XP
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
QQ, XQ
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
QR, XR
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
QS, XS
93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
QT, XT
106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
QU, XU
27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
R0, Y0
85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
R1, Y1
98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
R2, Y2
72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
R3, Y3
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
R4, Y4
71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
R5, Y5
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
R6, Y6
54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
R7, Y7
49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
R8, Y8
65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
R9, Y9
37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
RD, YD
276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
RE, YE
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
RF, YF
210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
RG, YG
182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
RH, YH
180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
RI, YI
148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
RN, YN
140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
RO, YO
122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
RP, YP
150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
RQ, YQ
141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
RR, YR
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
RS, YS
112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
RT, YT
146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
RU, YU
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
RV, YV
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
RW, YW
113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
RX, YX
96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
RY, YY
110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
RZ, YZ
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAQA, XA1522Thermus thermophilus HB8

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Entity ID: 22
MoleculeChainsLengthOrganism
P-site tRNAfMetQV, XV77Escherichia coli
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Entity ID: 23
MoleculeChainsLengthOrganism
mRNAQX, XX19Escherichia coli

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Entity ID: 24
MoleculeChainsLengthOrganism
A-site tRNAAla(GGC) U32-A38QY, XY76Escherichia coli

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Entity ID: 35
MoleculeChainsLengthOrganism
23S rRNARA, YA2915Thermus thermophilus HB8

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Entity ID: 36
MoleculeChainsLengthOrganism
5S rRNARB, YB122Thermus thermophilus HB8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

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QA, XA
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
SF4
Query on SF4

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QD, XD
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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QN, R4, R5, R6, R9, RY, XN, Y4, Y5, Y6, Y9, YY
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
QA, QB, QD, QE, QF, QG, QH, QI, QK, QL, QN, QO, QP, QT, QV, R0, R1, R3, R5, R6, R7, R9, RA, RB, RD, RE, RF, RG, RH, RN, RO, RP, RQ, RR, RT, RU, RV, RW, RZ, XA, XE, XF, XJ, XL, XR, XT, XV, XY, Y0, Y1, Y3, Y5, Y6, Y7, Y8, YA, YB, YD, YE, YF, YG, YI, YN, YO, YP, YQ, YR, YT, YV, YW
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
QL,XLL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.38α = 90
b = 445.83β = 90
c = 616.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM093278
National Science Foundation (NSF, United States)United StatesCHE 1808711

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references