Evidence: homology, Our collaborators have performed experiments using mutants at the interface and reported several reduce the stability and activity of the protein.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979351 Å / Relative weight: 1
Reflection
Resolution: 2.999→27.39 Å / Num. obs: 12803 / % possible obs: 99.18 % / Redundancy: 6.4 % / Biso Wilson estimate: 93.91 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 7.29
Reflection shell
Resolution: 3→3.107 Å / Num. unique obs: 1219 / CC1/2: 0.549 / CC star: 0.842
-
Processing
Software
Name
Version
Classification
PHENIX
1.18.2_3874
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SeMet-Rns Resolution: 3→27.39 Å / SU ML: 0.5667 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.8516 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The crystal has a pseudotranslational symmetry peak at fractional coordinates of 0.00 0.50 0.36 that is 45.7% of the origin peak from Patterson analysis.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3017
1279
10.03 %
Random selection
Rwork
0.2566
11472
-
-
obs
0.2611
12751
99.24 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 83.91 Å2
Refinement step
Cycle: LAST / Resolution: 3→27.39 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4044
0
24
0
4068
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.0123
4126
X-RAY DIFFRACTION
f_angle_d
1.3583
5528
X-RAY DIFFRACTION
f_chiral_restr
0.0718
636
X-RAY DIFFRACTION
f_plane_restr
0.0077
682
X-RAY DIFFRACTION
f_dihedral_angle_d
19.7813
1584
Refine LS restraints NCS
Type: Torsion NCS / Rms dev position: 0.666736622419 Å
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3-3.12
0.4513
134
0.4339
1209
X-RAY DIFFRACTION
96.83
3.12-3.26
0.3672
141
0.3446
1257
X-RAY DIFFRACTION
99.5
3.26-3.43
0.3743
140
0.3059
1260
X-RAY DIFFRACTION
99.36
3.43-3.65
0.3214
140
0.2968
1254
X-RAY DIFFRACTION
99.57
3.65-3.93
0.3005
140
0.2715
1260
X-RAY DIFFRACTION
99.57
3.93-4.32
0.2687
142
0.2408
1274
X-RAY DIFFRACTION
99.58
4.32-4.94
0.2796
143
0.2154
1278
X-RAY DIFFRACTION
99.58
4.95-6.22
0.3216
145
0.2714
1304
X-RAY DIFFRACTION
99.86
6.22-28.63
0.2741
154
0.2203
1376
X-RAY DIFFRACTION
99.29
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.21544454013
-0.540448111145
-1.95996930764
2.44661608328
-1.17689788509
4.85941847899
0.116131898836
-0.0251796823531
0.00413124036465
-0.317638275493
0.0173801216614
0.00251313023343
-0.0956960750855
-0.0946529871435
-0.109354456607
0.535532027167
-0.0713535701895
-0.0230628920774
0.497308186157
-0.074221818133
0.456887336842
-14.6984624648
-6.97811816203
7.13104502453
2
1.76461518609
1.38194746024
-1.14795057005
1.87281298888
-0.461387063377
4.03188224773
-0.295994122264
0.217426712525
-0.0435918301441
-1.26109028128
-0.126672615975
-0.549419110404
0.378013019803
-0.351315571638
0.449263341545
0.996463298275
0.112280950271
0.179015072631
0.793180577303
0.0308347705433
0.773241513018
-11.5299673349
-4.97734648555
-3.10730130099
3
2.28543275456
-0.290120961585
-0.100107522849
3.97736735255
1.61688846068
2.30679050438
0.060517578016
-0.102488740515
0.276260206016
-0.339666486744
-0.0497263937526
-0.157840983824
-0.376616278552
0.00434145219658
0.100491413004
0.412524502979
0.0125971003201
0.0359850149129
0.550608750228
0.0102265388689
0.563775440846
-12.2711387642
4.63470032523
15.8482716169
4
2.13683243077
-0.424460299219
1.38669140151
3.09838397313
-1.05921147936
3.36859060665
0.284797225357
-0.185583779736
0.175433266733
0.393473818061
-0.095641695486
0.168956196684
-0.36709058938
-0.562391435949
-0.16722827805
0.649500866603
0.0935265100511
0.124720060205
0.808980811432
-0.085938984101
0.644667054002
-38.462781726
7.99164862953
40.6575941758
5
3.43965175819
-0.5400972707
0.917397537067
3.43664172683
1.74896869542
3.93846332755
0.0245392364525
0.211124391989
0.278701186035
1.18282317401
-0.646417096507
0.208783196753
0.378123301344
-0.362966973121
0.405811530422
0.769420662204
-0.169260586134
-0.237474519349
0.761450979373
0.224241831415
0.65799633525
-34.0015259272
1.00702567456
48.7344352221
6
4.03886886026
-0.411638681838
-0.0243435406275
3.50830964996
-0.216113768892
1.68678215387
0.168979101014
0.401909709582
-0.59340843988
-0.0380530417565
-0.483558549622
0.532360058908
0.074687213046
-0.451981317986
0.287547291289
0.481708151703
0.017390659366
0.00920694069683
0.645592265563
-0.133282550317
0.608215435152
-38.0499441071
-4.14195092887
24.79144277
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION
ID
Refine TLS-ID
Selection details
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
chain 'A' and (resid9through91 )
A
A
9 - 91
1 - 83
2
2
chain 'A' and (resid92through129 )
A
A
92 - 129
84 - 119
3
3
chain 'A' and (resid130through263 )
A
A
130 - 263
120 - 253
4
4
chain 'B' and (resid9through91 )
B
B
9 - 91
1 - 83
5
5
chain 'B' and (resid92through173 )
B
B
92 - 173
84 - 163
6
6
chain 'B' and (resid174through263 )
B
B
174 - 263
164 - 253
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi