Resolution: 2.15→60.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.629 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Hydrogens have been added in the riding positions. There is some unexplained density at the 2-fold near B235-B236 main chain.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23539
1676
5 %
RANDOM
Rwork
0.18954
-
-
-
obs
0.19189
32122
97.96 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 31.282 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.99 Å2
0 Å2
0.85 Å2
2-
-
-1.2 Å2
0 Å2
3-
-
-
-0.68 Å2
Refinement step
Cycle: LAST / Resolution: 2.15→60.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4537
0
0
279
4816
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
4616
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
4267
X-RAY DIFFRACTION
r_angle_refined_deg
1.477
1.968
6254
X-RAY DIFFRACTION
r_angle_other_deg
0.862
3
9937
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.023
5
594
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.216
25.758
198
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.158
15
787
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.355
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.081
0.2
730
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
5174
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
886
X-RAY DIFFRACTION
r_nbd_refined
0.202
0.2
983
X-RAY DIFFRACTION
r_nbd_other
0.177
0.2
4503
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
2937
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.178
0.2
299
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.16
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.186
0.2
52
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.254
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
0.55
1.5
3053
X-RAY DIFFRACTION
r_mcbond_other
0.16
1.5
1222
X-RAY DIFFRACTION
r_mcangle_it
0.839
2
4757
X-RAY DIFFRACTION
r_scbond_it
1.559
3
1765
X-RAY DIFFRACTION
r_scangle_it
2.376
4.5
1497
X-RAY DIFFRACTION
r_nbtor_refined
0.181
0.2
2332
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.059
0.2
1
Refine LS restraints NCS
Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Number
Type
Rms dev position (Å)
Weight position
1
280
tightpositional
0.1
0.05
1
452
mediumpositional
0.57
0.5
1
280
tightthermal
0.15
0.5
1
452
mediumthermal
0.58
2
2
1466
tightpositional
0.08
0.05
2
2151
mediumpositional
0.47
0.5
2
1466
tightthermal
0.14
0.5
2
2151
mediumthermal
0.47
2
LS refinement shell
Resolution: 2.15→2.206 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.29
102
4.85 %
Rwork
0.238
2001
-
obs
-
-
83.72 %
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
1.4097
-0.1989
0.1364
5.3338
-1.908
2.3413
0.0077
0.0141
0.0273
0.1811
-0.0842
-0.356
0.0228
0.3008
0.0765
-0.2314
-0.0269
-0.0092
-0.1512
-0.0454
-0.1361
118.1258
8.1973
30.3153
2
2.2708
0.1257
-0.5773
3.3775
1.31
3.911
0.0962
0.2396
-0.1662
-0.6821
0.0196
-0.2459
-0.4551
0.1916
-0.1157
-0.0623
-0.0003
0.0584
-0.1675
-0.0598
-0.1186
119.9698
24.6232
10.3268
3
1.7284
-0.479
-1.6196
2.4665
2.1772
4.8066
-0.0406
0.0765
0.0013
-0.0761
-0.0369
0.0564
0.1516
-0.1963
0.0776
-0.2046
-0.015
0.0196
-0.197
-0.0395
-0.1624
108.5727
4.0896
30.333
4
2.538
0.787
0.6684
3.7947
-0.5269
2.9346
0.2518
-0.3016
-0.1608
0.4269
-0.0861
-0.0569
0.1483
-0.2322
-0.1657
-0.1548
-0.0267
-0.0241
-0.0935
-0.0762
-0.1765
103.0448
-0.687
54.1135
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
12 - 40
24 - 52
2
1
A
A
92 - 110
104 - 122
3
2
A
A
1 - 11
13 - 23
4
2
A
A
41 - 91
53 - 103
5
2
A
A
111 - 299
123 - 311
6
3
B
B
12 - 40
24 - 52
7
3
B
B
92 - 110
104 - 122
8
4
B
B
2 - 11
14 - 23
9
4
B
B
41 - 91
53 - 103
10
4
B
B
111 - 298
123 - 310
+
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