Evidence: gel filtration, Protein elutes as a monodisperse peak at the expected mass
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Method
PISA
Unit cell
Length a, b, c (Å)
41.253, 49.360, 41.239
Angle α, β, γ (deg.)
90.00, 104.30, 90.00
Int Tables number
4
Space group name H-M
P1211
-
Components
#1: Protein
SC_2L4HC2_23
Mass: 19030.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Computational design model Resolution: 1.74→22.52 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.84 Details: Iterative rounds of model building in Coot and refinement in Phenix.
Rfactor
Num. reflection
% reflection
Rfree
0.2658
1461
9.57 %
Rwork
0.2266
-
-
obs
0.2304
15269
92.07 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 58.9 Å2
Refinement step
Cycle: LAST / Resolution: 1.74→22.52 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1128
0
0
47
1175
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.019
1135
X-RAY DIFFRACTION
f_angle_d
1.448
1522
X-RAY DIFFRACTION
f_dihedral_angle_d
14.404
735
X-RAY DIFFRACTION
f_chiral_restr
0.072
185
X-RAY DIFFRACTION
f_plane_restr
0.008
199
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7401-1.8022
0.4204
121
0.3869
1120
X-RAY DIFFRACTION
76
1.8022-1.8743
0.3603
126
0.3235
1204
X-RAY DIFFRACTION
80
1.8743-1.9596
0.3414
133
0.2751
1271
X-RAY DIFFRACTION
86
1.9596-2.0629
0.2851
153
0.2535
1395
X-RAY DIFFRACTION
94
2.0629-2.192
0.3179
150
0.2237
1448
X-RAY DIFFRACTION
97
2.192-2.3611
0.2619
149
0.2186
1478
X-RAY DIFFRACTION
99
2.3611-2.5984
0.26
162
0.2179
1490
X-RAY DIFFRACTION
99
2.5984-2.9736
0.2527
162
0.2321
1493
X-RAY DIFFRACTION
100
2.9736-3.7437
0.2738
159
0.2193
1506
X-RAY DIFFRACTION
100
3.7437-22.5219
0.2435
146
0.2178
1403
X-RAY DIFFRACTION
91
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
4.0929
-0.7142
-1.8816
0.8143
1.3192
8.2398
0.3304
0.7844
0.2886
-0.2647
-0.3466
0.1158
-0.5885
-0.8759
-0.1795
0.4004
0.0513
-0.0659
0.4075
-0.0046
0.3999
7.2772
26.111
1.7753
2
8.5869
0.467
-2.89
1.9029
-0.547
4.7551
-0.0177
-0.6264
-0.4976
0.163
-0.192
0.2237
0.1743
-0.2752
0.438
0.3319
-0.0432
-0.0267
0.3528
-0.0535
0.3611
6.7535
18.7613
6.6441
3
3.7449
1.0898
-2.2556
2.0943
-1.6744
7.1105
0.6286
-1.4834
-0.57
0.5114
-0.7572
-0.3195
-0.2002
1.04
0.176
0.3925
-0.0381
-0.0704
0.4456
0.0514
0.3478
15.7223
21.7843
12.5267
4
5.9563
-0.1048
-3.9078
1.8233
0.182
7.72
0.3056
-0.3518
0.3726
0.2587
-0.1946
0.0775
-0.3192
-0.2349
-0.2005
0.3614
-0.0407
-0.0373
0.3528
-0.0507
0.3129
11.5684
29.3496
11.0825
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid1through35 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid36through73 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid79through112 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid113through151 )
+
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