Resolution: 2.5043→58.259 Å / SU ML: 0.3 Isotropic thermal model: Isotropic with TLS parameters for 2 groups σ(F): 2 / Phase error: 31.41 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2605
471
5.06 %
Rwork
0.2306
-
-
obs
0.2322
9317
99.82 %
all
-
9317
-
Solvent computation
Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.5043→58.259 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1459
0
3
19
1481
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
1494
X-RAY DIFFRACTION
f_angle_d
0.917
2029
X-RAY DIFFRACTION
f_dihedral_angle_d
14.75
553
X-RAY DIFFRACTION
f_chiral_restr
0.06
225
X-RAY DIFFRACTION
f_plane_restr
0.005
268
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.5043-2.8666
0.3198
148
0.2778
2867
X-RAY DIFFRACTION
100
2.8666-3.6116
0.2974
147
0.2544
2921
X-RAY DIFFRACTION
100
3.6116-58.2743
0.2362
176
0.2123
3058
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
3.9293
2.7754
-0.0873
8.1207
-0.4351
4.896
-0.0755
0.4765
0.095
-0.4616
0.0403
-0.3759
-0.0229
0.425
0.0718
0.2672
0.0526
0.0007
0.4986
0.0423
0.2806
40.8883
8.8979
24.98
2
1.0967
0.5513
-0.7487
4.9251
-3.0206
4.4886
0.1668
0.1774
0.3592
0.4264
0.2178
0.6725
-0.6925
-0.6268
-0.3311
0.3787
0.0761
0.1062
0.5422
0.1086
0.5803
34.3758
23.6706
27.2208
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid65:138)
2
X-RAY DIFFRACTION
2
(chainAandresid139:251)
+
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