Resolution: 2.6→2.7 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.63 / Num. unique all: 3598 / % possible all: 99.8
-
Processing
Software
Name
Version
Classification
PHENIX-AutoSol
modelbuilding
PHENIX
(phenix.refine: 1.8_1069)
refinement
XDS
datareduction
XSCALE
datascaling
PHENIX-AutoSol
phasing
Refinement
Method to determine structure: native data for SAD phase extension Resolution: 2.6→47.601 Å / SU ML: 0.3 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 23.98 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2267
1715
5.07 %
random
Rwork
0.1849
-
-
-
all
0.187
33951
-
-
obs
0.187
33844
99.71 %
-
Solvent computation
Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 76.8 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→47.601 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5800
0
80
80
5960
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
5960
X-RAY DIFFRACTION
f_angle_d
0.87
8104
X-RAY DIFFRACTION
f_dihedral_angle_d
12.773
2188
X-RAY DIFFRACTION
f_chiral_restr
0.056
961
X-RAY DIFFRACTION
f_plane_restr
0.004
1045
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.6-2.6929
0.2703
158
0.2408
3199
X-RAY DIFFRACTION
100
2.6929-2.8007
0.2786
162
0.2479
3143
X-RAY DIFFRACTION
100
2.8007-2.9282
0.2903
175
0.2486
3219
X-RAY DIFFRACTION
100
2.9282-3.0825
0.3094
172
0.2512
3150
X-RAY DIFFRACTION
100
3.0825-3.2756
0.2871
179
0.2357
3164
X-RAY DIFFRACTION
100
3.2756-3.5285
0.2527
182
0.1984
3221
X-RAY DIFFRACTION
100
3.5285-3.8834
0.2144
160
0.1816
3220
X-RAY DIFFRACTION
100
3.8834-4.445
0.2364
162
0.1634
3232
X-RAY DIFFRACTION
100
4.445-5.5988
0.1984
197
0.1575
3197
X-RAY DIFFRACTION
99
5.5988-47.6091
0.1837
168
0.1671
3384
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
5.898
2.6105
0.9226
7.2976
0.5756
5.2192
0.0123
-0.3029
-0.0708
0.7805
-0.0045
-0.1325
0.5555
0.5554
0.006
0.7211
0.2164
-0.0038
0.5297
0.0079
0.3826
54.3202
23.0267
211.7907
2
4.1333
-3.0311
-3.3405
4.7684
2.8988
4.4102
0.3994
0.2839
0.2857
-0.3
-0.2054
-0.1714
-0.3247
0.0782
-0.141
0.6249
0.0078
-0.0218
0.3852
0.0092
0.3295
42.4785
42.7519
203.9098
3
7.1178
1.0192
1.0991
5.3982
1.2633
4.3032
0.146
-0.0693
0.9728
0.1022
-0.0871
-0.4192
-0.7119
0.89
-0.0688
0.7408
-0.211
0.1264
0.5057
-0.072
0.6322
51.5821
56.6928
218.7072
4
6.2947
1.6778
-0.0468
7.6899
1.6046
3.9236
-0.0987
0.4143
-0.4539
-0.929
0.2263
0.3493
0.5141
-0.3202
-0.053
0.9735
-0.2924
-0.0983
0.3955
0.0185
0.5833
9.0677
24.0085
235.1534
5
2.5757
2.0978
-2.0524
3.4384
-1.9738
3.2628
0.4049
-0.4088
0.2386
0.3025
-0.2972
0.1354
-0.3201
0.134
-0.0544
0.8172
-0.2491
-0.0008
0.3979
-0.0125
0.5087
21.355
44.8429
240.2534
6
8.3046
-1.7911
0.1826
5.0538
-2.1233
5.9573
0.4304
0.1975
0.3803
0.0444
-0.0326
0.4685
-0.4584
-1.0922
-0.2885
0.6715
-0.0597
0.1046
0.4476
0.0546
0.5002
11.2921
55.4753
223.6542
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resseq14:117)
2
X-RAY DIFFRACTION
2
chain 'A' and (resseq118:263)
3
X-RAY DIFFRACTION
3
chain 'A' and (resseq264:398)
4
X-RAY DIFFRACTION
4
chain 'B' and (resseq15:118)
5
X-RAY DIFFRACTION
5
chain 'B' and (resseq119:263)
6
X-RAY DIFFRACTION
6
chain 'B' and (resseq264:398)
+
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