Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 2.3→44.31 Å / Num. obs: 38287 / % possible obs: 99.86 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.1766 / Net I/σ(I): 6.95
Reflection shell
Resolution: 2.3→2.382 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.9439 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3775 / % possible all: 99.79
-
Processing
Software
Name
Version
Classification
REFMAC
5
refinement
DIALS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / SU B: 20.306 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23664
1996
5.2 %
RANDOM
Rwork
0.20935
-
-
-
obs
0.21085
36286
99.97 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 63.721 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.19 Å2
0 Å2
0 Å2
2-
-
-2.59 Å2
-0 Å2
3-
-
-
2.4 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→44.31 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4874
0
231
128
5233
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.016
5251
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.015
4811
X-RAY DIFFRACTION
r_angle_refined_deg
1.768
1.841
7233
X-RAY DIFFRACTION
r_angle_other_deg
0.535
1.606
11107
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.819
5.36
709
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.656
10
729
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
834
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
6179
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1063
X-RAY DIFFRACTION
r_mcbond_it
1.636
1.857
2625
X-RAY DIFFRACTION
r_mcbond_other
1.624
1.855
2623
X-RAY DIFFRACTION
r_mcangle_it
2.685
2.769
3272
X-RAY DIFFRACTION
r_mcangle_other
2.685
2.77
3273
X-RAY DIFFRACTION
r_scbond_it
1.711
1.964
2626
X-RAY DIFFRACTION
r_scbond_other
1.691
1.964
2626
X-RAY DIFFRACTION
r_scangle_other
2.708
2.885
3957
X-RAY DIFFRACTION
r_long_range_B_refined
6.267
24.286
5877
X-RAY DIFFRACTION
r_long_range_B_other
6.269
24.175
5857
LS refinement shell
Resolution: 2.3→2.359 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.314
161
-
Rwork
0.314
2612
-
obs
-
-
99.96 %
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
3.1792
1.162
0.4315
2.2111
0.174
3.225
-0.1633
0.3365
0.1342
-0.2691
0.001
0.1853
-0.187
-0.1934
0.1623
0.2918
-0.0104
-0.0497
0.5695
-0.0309
0.0254
-23.971
-33.291
8.653
2
2.3177
0.2601
-0.1584
2.0187
0.7293
2.3021
0.0653
-0.0774
0.2874
0.1305
-0.143
0.0642
-0.2957
-0.3997
0.0777
0.339
0.0288
-0.0231
0.6838
-0.0254
0.041
-22.045
-22.882
31.855
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 403
2
X-RAY DIFFRACTION
2
B
2 - 402
+
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