Resolution: 2.4→45.8 Å / Num. obs: 20785 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shell
Resolution: 2.4→2.5 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.24 / % possible all: 90.1
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE: 1.8.2_1309)
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: MOLECULAR REPLACEMENT MODEL FROM PARTIAL MODEL BUILT FROM LOW-RESOLUTION SEMET DATASET. Resolution: 2.397→45.839 Å / SU ML: 0.34 / σ(F): 1.99 / Phase error: 30.71 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2379
1036
5 %
Rwork
0.1891
-
-
obs
0.1915
20749
98.59 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.397→45.839 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3002
0
60
102
3164
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
3128
X-RAY DIFFRACTION
f_angle_d
1.102
4230
X-RAY DIFFRACTION
f_dihedral_angle_d
19.242
1143
X-RAY DIFFRACTION
f_chiral_restr
0.075
463
X-RAY DIFFRACTION
f_plane_restr
0.004
546
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3971-2.5235
0.4255
140
0.3551
2611
X-RAY DIFFRACTION
93
2.5235-2.6816
0.3591
146
0.2943
2773
X-RAY DIFFRACTION
99
2.6816-2.8886
0.3062
148
0.2348
2792
X-RAY DIFFRACTION
99
2.8886-3.1792
0.3165
146
0.2371
2833
X-RAY DIFFRACTION
100
3.1792-3.6391
0.2518
148
0.2068
2825
X-RAY DIFFRACTION
99
3.6391-4.5842
0.2062
151
0.1592
2874
X-RAY DIFFRACTION
100
4.5842-45.8473
0.198
157
0.1594
3005
X-RAY DIFFRACTION
100
+
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