Resolution: 1.8→76.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.431 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24369
2139
5 %
RANDOM
Rwork
0.20351
-
-
-
obs
0.20561
40989
98.03 %
-
Solvent computation
Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parameters
Biso mean: 38.766 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.23 Å2
0.12 Å2
0 Å2
2-
-
0.23 Å2
-0 Å2
3-
-
-
-0.76 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→76.48 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2431
0
0
187
2618
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.019
2706
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2459
X-RAY DIFFRACTION
r_angle_refined_deg
1.418
1.877
3672
X-RAY DIFFRACTION
r_angle_other_deg
1.139
2.935
5748
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.31
5
335
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.349
24.328
134
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.198
15
497
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.843
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.087
0.2
386
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
3049
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
561
X-RAY DIFFRACTION
r_mcbond_it
5.401
3.603
1304
X-RAY DIFFRACTION
r_mcbond_other
5.38
3.598
1303
X-RAY DIFFRACTION
r_mcangle_it
7.273
5.376
1648
X-RAY DIFFRACTION
r_mcangle_other
7.272
5.383
1649
X-RAY DIFFRACTION
r_scbond_it
6.579
4.152
1402
X-RAY DIFFRACTION
r_scbond_other
6.576
4.157
1403
X-RAY DIFFRACTION
r_scangle_other
9.034
5.995
2024
X-RAY DIFFRACTION
r_long_range_B_refined
11.207
43.64
3194
X-RAY DIFFRACTION
r_long_range_B_other
11.235
43.398
3152
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.411
77
-
Rwork
0.411
2278
-
obs
-
-
73.82 %
+
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