4V4Q

Crystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.279 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history. 


Literature

Structures of the bacterial ribosome at 3.5 A resolution.

Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., Cate, J.H.

(2005) Science 310: 827-834

  • DOI: https://doi.org/10.1126/science.1117230
  • Primary Citation of Related Structures:  
    4V4Q

  • PubMed Abstract: 

    We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.

    • Organizational Affiliation: 

    Department of Chemistry, University of California, Berkeley, CA 94720, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth AC],
BB [auth CC]		232Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth AD],
CB [auth CD]		205Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth AE],
DB [auth CE]		166Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth AF],
EB [auth CF]		135Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth AG],
FB [auth CG]		178Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth AH],
GB [auth CH]		129Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth AI],
HB [auth CI]		129Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth AJ],
IB [auth CJ]		103Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth AK],
JB [auth CK]		128Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth AL],
KB [auth CL]		123Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth AM],
LB [auth CM]		117Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14M [auth AN],
MB [auth CN]		100Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth AO],
NB [auth CO]		89Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth AP],
OB [auth CP]		82Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth AQ],
PB [auth CQ]		83Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth AR],
QB [auth CR]		74Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth AS],
RB [auth CS]		91Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth AT],
SB [auth CT]		86Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2T [auth AB],
TB [auth CB]		240Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth AU],
UB [auth CU]		71Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25X [auth BV],
XB [auth DV]		94Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth BC],
YB [auth DC]		273Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth BD],
ZB [auth DD]		209Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth BE],
AC [auth DE]		201Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth BF],
BC [auth DF]		178Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth BG],
CC [auth DG]		176Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9DA [auth BH],
DC [auth DH]		149Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth BJ],
EC [auth DJ]		142Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14FA [auth BK],
FC [auth DK]		123Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth BL],
GC [auth DL]		144Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16HA [auth BM],
HC [auth DM]		136Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17IA [auth BN],
IC [auth DN]		127Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18JA [auth BO],
JC [auth DO]		117Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19KA [auth BP],
KC [auth DP]		114Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth BQ],
LC [auth DQ]		117Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21MA [auth BR],
MC [auth DR]		103Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth BS],
NC [auth DS]		110Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth BT],
OC [auth DT]		100Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth BU],
PC [auth DU]		103Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27QA [auth BW],
QC [auth DW]		84Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29RA [auth BX],
RC [auth DX]		63Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30SA [auth BY],
SC [auth DY]		58Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31TA [auth BZ],
TC [auth DZ]		70Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32UA [auth B0],
UC [auth D0]		56Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33VA [auth B1],
VC [auth D1]		54Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34WA [auth B2],
WC [auth D2]		46Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35XA [auth B3],
XC [auth D3]		64Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36YA [auth B4],
YC [auth D4]		38Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11ZA [auth BI],
ZC [auth DI]		141Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA],
AB [auth CA]		1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
5S ribosomal RNAV [auth BA],
VB [auth DA]		120Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S ribosomal RNAW [auth BB],
WB [auth DB]		2,904Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
AD [auth AA]
AE [auth AA]
AF [auth AA]
AG [auth BB]
AH [auth BB]
AD [auth AA],
AE [auth AA],
AF [auth AA],
AG [auth BB],
AH [auth BB],
AI [auth BB],
AJ [auth BB],
AK [auth CA],
AL [auth CA],
AM [auth DB],
AN [auth DB],
AO [auth DB],
AP [auth DB],
AQ [auth DB],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth BB],
BH [auth BB],
BI [auth BB],
BJ [auth BB],
BK [auth CA],
BL [auth CA],
BM [auth DB],
BN [auth DB],
BO [auth DB],
BP [auth DB],
BQ [auth DB],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth BB],
CH [auth BB],
CI [auth BB],
CJ [auth BB],
CK [auth CA],
CL [auth CA],
CM [auth DB],
CN [auth DB],
CO [auth DB],
CP [auth DB],
CQ [auth DB],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth BB],
DH [auth BB],
DI [auth BB],
DJ [auth BB],
DK [auth CA],
DL [auth CA],
DM [auth DB],
DN [auth DB],
DO [auth DB],
DP [auth DB],
DQ [auth DB],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth BB],
EH [auth BB],
EI [auth BB],
EJ [auth BB],
EK [auth CA],
EL [auth CA],
EM [auth DB],
EN [auth DB],
EO [auth DB],
EP [auth DB],
EQ [auth DN],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth BB],
FH [auth BB],
FI [auth BB],
FJ [auth BB],
FK [auth CA],
FL [auth CA],
FM [auth DB],
FN [auth DB],
FO [auth DB],
FP [auth DB],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BB],
GH [auth BB],
GI [auth BB],
GJ [auth BB],
GK [auth CA],
GL [auth CA],
GM [auth DB],
GN [auth DB],
GO [auth DB],
GP [auth DB],
HD [auth AA],
HE [auth AA],
HF [auth AP],
HG [auth BB],
HH [auth BB],
HI [auth BB],
HJ [auth BB],
HK [auth CA],
HL [auth CA],
HM [auth DB],
HN [auth DB],
HO [auth DB],
HP [auth DB],
ID [auth AA],
IE [auth AA],
IF [auth BB],
IG [auth BB],
IH [auth BB],
II [auth BB],
IJ [auth BB],
IK [auth CA],
IL [auth CA],
IM [auth DB],
IN [auth DB],
IO [auth DB],
IP [auth DB],
JD [auth AA],
JE [auth AA],
JF [auth BB],
JG [auth BB],
JH [auth BB],
JI [auth BB],
JJ [auth BB],
JK [auth CA],
JL [auth CA],
JM [auth DB],
JN [auth DB],
JO [auth DB],
JP [auth DB],
KD [auth AA],
KE [auth AA],
KF [auth BB],
KG [auth BB],
KH [auth BB],
KI [auth BB],
KJ [auth BB],
KK [auth CA],
KL [auth CA],
KM [auth DB],
KN [auth DB],
KO [auth DB],
KP [auth DB],
LD [auth AA],
LE [auth AA],
LF [auth BB],
LG [auth BB],
LH [auth BB],
LI [auth BB],
LJ [auth BB],
LK [auth CA],
LL [auth CA],
LM [auth DB],
LN [auth DB],
LO [auth DB],
LP [auth DB],
MD [auth AA],
ME [auth AA],
MF [auth BB],
MG [auth BB],
MH [auth BB],
MI [auth BB],
MJ [auth BB],
MK [auth CA],
ML [auth CA],
MM [auth DB],
MN [auth DB],
MO [auth DB],
MP [auth DB],
ND [auth AA],
NE [auth AA],
NF [auth BB],
NG [auth BB],
NH [auth BB],
NI [auth BB],
NJ [auth BB],
NK [auth CA],
NL [auth CA],
NM [auth DB],
NN [auth DB],
NO [auth DB],
NP [auth DB],
OD [auth AA],
OE [auth AA],
OF [auth BB],
OG [auth BB],
OH [auth BB],
OI [auth BB],
OJ [auth CA],
OK [auth CA],
OL [auth CA],
OM [auth DB],
ON [auth DB],
OO [auth DB],
OP [auth DB],
PD [auth AA],
PE [auth AA],
PF [auth BB],
PG [auth BB],
PH [auth BB],
PI [auth BB],
PJ [auth CA],
PK [auth CA],
PL [auth CA],
PM [auth DB],
PN [auth DB],
PO [auth DB],
PP [auth DB],
QD [auth AA],
QE [auth AA],
QF [auth BB],
QG [auth BB],
QH [auth BB],
QI [auth BB],
QJ [auth CA],
QK [auth CA],
QL [auth CA],
QM [auth DB],
QN [auth DB],
QO [auth DB],
QP [auth DB],
RD [auth AA],
RE [auth AA],
RF [auth BB],
RG [auth BB],
RH [auth BB],
RI [auth BB],
RJ [auth CA],
RK [auth CA],
RL [auth CA],
RM [auth DB],
RN [auth DB],
RO [auth DB],
RP [auth DB],
SD [auth AA],
SE [auth AA],
SF [auth BB],
SG [auth BB],
SH [auth BB],
SI [auth BB],
SJ [auth CA],
SK [auth CA],
SL [auth CA],
SM [auth DB],
SN [auth DB],
SO [auth DB],
SP [auth DB],
TD [auth AA],
TE [auth AA],
TF [auth BB],
TG [auth BB],
TH [auth BB],
TI [auth BB],
TJ [auth CA],
TK [auth CA],
TL [auth CA],
TM [auth DB],
TN [auth DB],
TO [auth DB],
TP [auth DB],
UD [auth AA],
UE [auth AA],
UF [auth BB],
UG [auth BB],
UH [auth BB],
UI [auth BB],
UJ [auth CA],
UK [auth CA],
UL [auth CA],
UM [auth DB],
UN [auth DB],
UO [auth DB],
UP [auth DB],
VD [auth AA],
VE [auth AA],
VF [auth BB],
VG [auth BB],
VH [auth BB],
VI [auth BB],
VJ [auth CA],
VK [auth CA],
VL [auth CA],
VM [auth DB],
VN [auth DB],
VO [auth DB],
VP [auth DB],
WD [auth AA],
WE [auth AA],
WF [auth BB],
WG [auth BB],
WH [auth BB],
WI [auth BB],
WJ [auth CA],
WK [auth CA],
WL [auth CA],
WM [auth DB],
WN [auth DB],
WO [auth DB],
WP [auth DB],
XD [auth AA],
XE [auth AA],
XF [auth BB],
XG [auth BB],
XH [auth BB],
XI [auth BB],
XJ [auth CA],
XK [auth CA],
XL [auth CA],
XM [auth DB],
XN [auth DB],
XO [auth DB],
XP [auth DB],
YD [auth AA],
YE [auth AA],
YF [auth BB],
YG [auth BB],
YH [auth BB],
YI [auth BB],
YJ [auth CA],
YK [auth CA],
YL [auth DB],
YM [auth DB],
YN [auth DB],
YO [auth DB],
YP [auth DB],
ZD [auth AA],
ZE [auth AA],
ZF [auth BB],
ZG [auth BB],
ZH [auth BB],
ZI [auth BB],
ZJ [auth CA],
ZK [auth CA],
ZL [auth DB],
ZM [auth DB],
ZN [auth DB],
ZO [auth DB],
ZP [auth DB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.279 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.85α = 90
b = 379.2β = 90
c = 739.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description