Resolution: 2.104→2.22 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4 / Num. unique all: 3498 / % possible all: 99.3
-
Processing
Software
Name
Version
Classification
MAR345dtb
datacollection
PHENIX
(phenix.autosol)
modelbuilding
PHENIX
(phenix.refine: 1.6_289)
refinement
XSCALE
datascaling
SCALA
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.104→50.678 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic with TLS restraints / σ(F): 1.13 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2574
2220
4.94 %
Random
Rwork
0.2101
-
-
-
obs
0.2124
23106
97.73 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.464 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Biso mean: 45.83 Å2
Baniso -1
Baniso -2
Baniso -3
1-
14.0832 Å2
-0 Å2
-0 Å2
2-
-
-11.7579 Å2
-0 Å2
3-
-
-
-2.3252 Å2
Refine analyze
Luzzati coordinate error obs: 0.29 Å
Refinement step
Cycle: LAST / Resolution: 2.104→50.678 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2317
0
49
146
2512
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
2445
X-RAY DIFFRACTION
f_angle_d
1.023
3285
X-RAY DIFFRACTION
f_dihedral_angle_d
16.866
955
X-RAY DIFFRACTION
f_chiral_restr
0.072
380
X-RAY DIFFRACTION
f_plane_restr
0.004
410
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
925
X-RAY DIFFRACTION
POSITIONAL
1
2
B
925
X-RAY DIFFRACTION
POSITIONAL
0.05
LS refinement shell
Refine-ID: X-RAY DIFFRACTION
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
% reflection obs (%)
2.1039-2.1791
0.3451
228
0.2849
4223
4464
97
2.1791-2.2663
0.3151
220
0.2629
4304
4533
98
2.2663-2.3695
0.2829
224
0.2379
4306
4551
98
2.3695-2.4944
0.271
224
0.2228
4285
4515
98
2.4944-2.6507
0.3172
225
0.2102
4318
4549
98
2.6507-2.8553
0.2804
220
0.2159
4299
4530
99
2.8553-3.1426
0.2655
222
0.22
4292
4519
98
3.1426-3.5972
0.2861
223
0.2094
4294
4519
98
3.5972-4.5317
0.1988
216
0.1757
4216
4433
97
4.5317-50.6928
0.205
218
0.1832
4224
4451
96
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
0.249
-0.102
0.2464
2.9324
0.752
1.6826
0.0321
-0.0191
-0.046
0.1499
0.034
-0.0734
0.0768
-0.0275
-0.0618
0.1255
-0.0111
0.0268
0.1823
0.0062
0.1892
1.0494
-9.2904
16.1836
2
0.764
0.0706
-0.2048
2.211
0.2686
1.4614
0.1011
0.0843
0.1344
-0.3569
0.0514
-0.2524
-0.2358
0.1155
-0.1325
0.291
-0.0067
0.0079
0.1816
0.0023
0.24
0.4763
-2.1058
-15.7368
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