Resolution: 1.9→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4508 / % possible all: 97
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SnB
phasing
PHENIX
modelbuilding
PHENIX
(phenix.refine: 1.5_2)
refinement
DENZO
datareduction
SCALEPACK
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.895→36.691 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2183
2292
5.1 %
RANDOM
Rwork
0.2011
-
-
-
obs
0.202
44926
99.32 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.917 Å2 / ksol: 0.4 e/Å3
Refinement step
Cycle: LAST / Resolution: 1.895→36.691 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1388
0
0
182
1570
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.043
1408
X-RAY DIFFRACTION
f_angle_d
1.582
1914
X-RAY DIFFRACTION
f_dihedral_angle_d
17.803
514
X-RAY DIFFRACTION
f_chiral_restr
0.106
226
X-RAY DIFFRACTION
f_plane_restr
0.013
254
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.895-1.9363
0.2461
156
0.2551
2489
X-RAY DIFFRACTION
94
1.9363-1.9813
0.2648
136
0.2193
2683
X-RAY DIFFRACTION
100
1.9813-2.0308
0.2206
137
0.2134
2703
X-RAY DIFFRACTION
100
2.0308-2.0857
0.2287
131
0.2084
2701
X-RAY DIFFRACTION
100
2.0857-2.1471
0.2487
140
0.2018
2687
X-RAY DIFFRACTION
100
2.1471-2.2164
0.2038
150
0.1944
2682
X-RAY DIFFRACTION
100
2.2164-2.2956
0.2696
132
0.188
2690
X-RAY DIFFRACTION
100
2.2956-2.3875
0.1845
166
0.181
2642
X-RAY DIFFRACTION
100
2.3875-2.4961
0.2509
148
0.1936
2667
X-RAY DIFFRACTION
100
2.4961-2.6277
0.191
141
0.2044
2705
X-RAY DIFFRACTION
100
2.6277-2.7923
0.2274
129
0.2238
2675
X-RAY DIFFRACTION
100
2.7923-3.0078
0.215
163
0.227
2685
X-RAY DIFFRACTION
100
3.0078-3.3103
0.2439
130
0.2069
2696
X-RAY DIFFRACTION
100
3.3103-3.7889
0.1989
149
0.1763
2662
X-RAY DIFFRACTION
100
3.7889-4.7719
0.1787
151
0.1612
2664
X-RAY DIFFRACTION
99
4.7719-36.6979
0.2175
133
0.2219
2603
X-RAY DIFFRACTION
97
Refinement TLS params.
Refine-ID: X-RAY DIFFRACTION
ID
Method
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
refined
0.7405
0.7109
-1.2874
0.5886
-0.059
0.9704
-0.1433
0.0763
0.0788
-0.022
0.032
-0.0198
0.0456
-0.0803
0.0504
0.0347
0.0082
0.0145
0.0641
0.0061
0.0395
26.2547
41.6815
44.1179
2
0.9022
-0.2574
0.286
0.5748
0.5933
2.1371
-0.006
0.025
-0.0067
-0.0501
0.0053
-0.0043
-0.1167
-0.0431
0.0003
0.0478
-0.0064
-0.0115
0.0339
0.01
0.0433
Refinement TLS group
Selection details: chain B
+
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