Resolution: 2.41→40.746 Å / SU ML: 0.68 / σ(F): 2 / Phase error: 21.78 / Stereochemistry target values: ML Details: SOFT TORSION NCS RESTRAINTS WERE ENFORCED IN REFINEMENT BETWEEN THE TWO MOLECULES IN THE ASYMMETRIC UNIT.
Rfactor
Num. reflection
% reflection
Rfree
0.2298
1717
3.4 %
Rwork
0.1874
-
-
obs
0.1888
51080
99.94 %
Solvent computation
Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.939 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Biso mean: 32.7 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.1386 Å2
0 Å2
0 Å2
2-
-
-3.4775 Å2
0 Å2
3-
-
-
-1.6611 Å2
Refinement step
Cycle: LAST / Resolution: 2.41→40.746 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8799
0
5
442
9246
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
9199
X-RAY DIFFRACTION
f_angle_d
0.944
12507
X-RAY DIFFRACTION
f_dihedral_angle_d
12.79
3429
X-RAY DIFFRACTION
f_chiral_restr
0.066
1397
X-RAY DIFFRACTION
f_plane_restr
0.004
1600
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
563
X-RAY DIFFRACTION
POSITIONAL
1
2
B
563
X-RAY DIFFRACTION
POSITIONAL
0.309
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.41-2.4809
0.2728
141
0.247
4028
X-RAY DIFFRACTION
100
2.4809-2.561
0.3133
144
0.2383
4066
X-RAY DIFFRACTION
100
2.561-2.6525
0.2479
142
0.2311
4080
X-RAY DIFFRACTION
100
2.6525-2.7587
0.2609
141
0.2064
4060
X-RAY DIFFRACTION
100
2.7587-2.8842
0.2488
144
0.21
4075
X-RAY DIFFRACTION
100
2.8842-3.0362
0.2564
142
0.2022
4079
X-RAY DIFFRACTION
100
3.0362-3.2264
0.2625
139
0.1947
4091
X-RAY DIFFRACTION
100
3.2264-3.4754
0.2324
144
0.1807
4105
X-RAY DIFFRACTION
100
3.4754-3.8249
0.1926
142
0.1671
4113
X-RAY DIFFRACTION
100
3.8249-4.3778
0.1943
143
0.1536
4136
X-RAY DIFFRACTION
100
4.3778-5.5134
0.2108
142
0.1604
4190
X-RAY DIFFRACTION
100
5.5134-40.7514
0.2151
153
0.1912
4340
X-RAY DIFFRACTION
100
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
0.2831
-0.0262
0.015
0.1049
-0.0749
0.4767
0.0205
0.0304
0.1054
0.04
0.0225
0.0495
0.1619
0.084
0.044
0.2697
0.0533
-0.0297
0.0704
-0.0032
-0.0053
-4.3553
24.2154
-25.6812
2
0.2578
-0.015
0.0462
0.1687
0.0633
0.4441
0.0031
-0.0438
0.0255
0.0206
-0.042
0.0023
-0.0634
-0.0667
-0.0685
0.2348
-0.0196
0.0015
0.0703
0.0293
0.0292
-46.6546
51.3576
-32.2092
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
+
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