Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9786 Å / Relative weight: 1
Reflection
Resolution: 1.76→39.025 Å / Num. obs: 12091 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 46
Reflection shell
Resolution: 1.76→1.8 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 14.4 / % possible all: 100
-
Processing
Software
Name
Version
Classification
PHENIX
(dev_2299: ???)
refinement
MOSFLM
7.0.9
datareduction
Aimless
0.1.27
datascaling
SOLVE
2.13
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.762→39.025 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.44 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1971
573
4.76 %
RANDOM
Rwork
0.1673
-
-
-
obs
0.1687
12049
99.74 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.762→39.025 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
837
0
7
94
938
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
888
X-RAY DIFFRACTION
f_angle_d
0.871
1204
X-RAY DIFFRACTION
f_dihedral_angle_d
15.975
545
X-RAY DIFFRACTION
f_chiral_restr
0.054
127
X-RAY DIFFRACTION
f_plane_restr
0.006
161
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7622-1.9395
0.2207
133
0.1712
2859
X-RAY DIFFRACTION
100
1.9395-2.2201
0.2039
171
0.1573
2836
X-RAY DIFFRACTION
100
2.2201-2.797
0.199
140
0.1764
2879
X-RAY DIFFRACTION
100
2.797-39.0345
0.1879
129
0.1657
2902
X-RAY DIFFRACTION
99
Refinement TLS params.
Method: refined / Origin x: 9.3645 Å / Origin y: 38.7663 Å / Origin z: 18.6899 Å
11
12
13
21
22
23
31
32
33
T
0.1215 Å2
0.0037 Å2
-0.0036 Å2
-
0.1004 Å2
0.0027 Å2
-
-
0.131 Å2
L
2.3535 °2
-0.1389 °2
-0.0148 °2
-
2.5756 °2
-0.3736 °2
-
-
1.3337 °2
S
0.0288 Å °
0.0652 Å °
-0.0149 Å °
-0.1527 Å °
-0.0471 Å °
0.0757 Å °
0.069 Å °
-0.0198 Å °
-0.0169 Å °
Refinement TLS group
Selection details: all
+
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