Resolution: 1.853→72.85 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.213 / SU Rfree Blow DPI: 0.157 Details: Automated non-crystallographic restraints were used throughtout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ...Details: Automated non-crystallographic restraints were used throughtout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ratio mixture of Cys and Cys S-Sulfonic acid was initially modelled in Fo-Fc residual density. At each Cys152 site, occupancies for Cys and Cys S-Sulfonic acid were refined and constrained so that they sum up to 1.000. External secondary structure restraints to PDB ID 6YND.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2066
4059
-
RANDOM
Rwork
0.1903
-
-
-
obs
0.1911
81457
67.6 %
-
Displacement parameters
Biso mean: 30.35 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.1261 Å2
0 Å2
0.5176 Å2
2-
-
0.4886 Å2
0 Å2
3-
-
-
-1.6147 Å2
Refine analyze
Luzzati coordinate error obs: 0.26 Å
Refinement step
Cycle: LAST / Resolution: 1.853→72.85 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10108
0
173
569
10850
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.008
20928
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.05
37896
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
6308
SINUSOIDAL
2
X-RAY DIFFRACTION
t_gen_planes
3340
HARMONIC
5
X-RAY DIFFRACTION
t_it
10529
HARMONIC
10
X-RAY DIFFRACTION
t_chiral_improper_torsion
1388
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_ideal_dist_contact
16210
SEMIHARMONIC
4
X-RAY DIFFRACTION
t_omega_torsion
3.71
X-RAY DIFFRACTION
t_other_torsion
15.61
LS refinement shell
Resolution: 1.853→1.98 Å
Rfactor
Num. reflection
% reflection
Rfree
0.2198
94
-
Rwork
0.2182
-
-
obs
-
-
7.29 %
+
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