Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9775 Å / Relative weight: 1
Reflection
Resolution: 1.84→50 Å / Num. obs: 61578 / % possible obs: 100 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.211 / Rsym value: 0.083 / Net I/σ(I): 9.3
Reflection shell
Highest resolution: 1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.93 / Rsym value: 0.85 / % possible all: 100
-
Processing
Software
Name
Version
Classification
PHENIX
(phenix.refine: 1.8.4_1496)
refinement
HKL-2000
datascaling
Coot
modelbuilding
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: MAD data set of the same MxaA Reductase construct Resolution: 1.899→41.82 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.83 / Stereochemistry target values: TWIN_LSQ_F Details: Good quality data could only be collected with SeMet crystals. We initially solved the structure by MAD and used SeMet crystals to collect single wavelength experiments for molecular replacement.
Rfactor
Num. reflection
% reflection
Rfree
0.2034
1997
3.25 %
Rwork
0.1582
-
-
obs
0.1617
61518
99.9 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.899→41.82 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6034
0
104
502
6640
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
6275
X-RAY DIFFRACTION
f_angle_d
0.976
8540
X-RAY DIFFRACTION
f_dihedral_angle_d
14.797
2366
X-RAY DIFFRACTION
f_chiral_restr
0.036
980
X-RAY DIFFRACTION
f_plane_restr
0.004
1097
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9004-1.9479
0.2928
141
0.2659
4172
X-RAY DIFFRACTION
97
1.9479-2.0005
0.2898
146
0.2493
4218
X-RAY DIFFRACTION
97
2.0005-2.0594
0.2563
143
0.2419
4287
X-RAY DIFFRACTION
97
2.0594-2.1258
0.2526
142
0.2385
4256
X-RAY DIFFRACTION
97
2.1258-2.2018
0.24
140
0.2346
4216
X-RAY DIFFRACTION
97
2.2018-2.2899
0.2267
142
0.2145
4231
X-RAY DIFFRACTION
97
2.2899-2.394
0.3009
141
0.2105
4245
X-RAY DIFFRACTION
97
2.394-2.5202
0.2723
147
0.1973
4251
X-RAY DIFFRACTION
97
2.5202-2.6779
0.2002
144
0.187
4268
X-RAY DIFFRACTION
97
2.6779-2.8845
0.2055
142
0.1805
4232
X-RAY DIFFRACTION
97
2.8845-3.1743
0.1988
140
0.1591
4258
X-RAY DIFFRACTION
97
3.1743-3.6327
0.1818
141
0.1292
4281
X-RAY DIFFRACTION
97
3.6327-4.573
0.1515
143
0.1009
4245
X-RAY DIFFRACTION
97
4.573-26.5904
0.1726
143
0.1016
4300
X-RAY DIFFRACTION
97
+
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