Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2009
Radiation
Monochromator: Side scattering bent cube-root I-beam single crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97939 Å / Relative weight: 1
Reflection
Redundancy: 3.4 % / Av σ(I) over netI: 14.44 / Number: 133153 / Rmerge(I) obs: 0.078 / Χ2: 1.04 / D res high: 2.9 Å / D res low: 45 Å / Num. obs: 39294 / % possible obs: 88.4
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
6.24
45
99.6
1
0.048
0.974
3.6
4.96
6.24
100
1
0.065
1.042
3.7
4.33
4.96
100
1
0.07
1.003
3.6
3.94
4.33
100
1
0.08
1.035
3.6
3.65
3.94
99.6
1
0.104
1.084
3.5
3.44
3.65
98.4
1
0.134
1.06
3.3
3.27
3.44
92.5
1
0.181
1.069
3.3
3.12
3.27
81.9
1
0.217
1.079
3.1
3
3.12
64.4
1
0.262
1.023
2.9
2.9
3
46.9
1
0.322
0.998
2.7
Reflection
Resolution: 2.9→45 Å / Num. obs: 39294 / % possible obs: 88.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
% possible all
2.9-3
2.7
0.322
46.9
3-3.12
2.9
0.262
64.4
3.12-3.27
3.1
0.217
81.9
3.27-3.44
3.3
0.181
92.5
3.44-3.65
3.3
0.134
98.4
3.65-3.94
3.5
0.104
99.6
3.94-4.33
3.6
0.08
100
4.33-4.96
3.6
0.07
100
4.96-6.24
3.7
0.065
100
6.24-45
3.6
0.048
99.6
-
Phasing
Phasing
Method: molecular replacement
Phasing MR
Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
2.75 Å
49.44 Å
Translation
2.75 Å
49.44 Å
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
1.3.3
phasing
PHENIX
1.6.2_432
refinement
PDB_EXTRACT
3.1
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.437 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.43 / σ(F): 1.91 / Phase error: 34.5 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2896
1991
5.08 %
Rwork
0.2217
-
-
obs
0.2252
39216
88.12 %
Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.863 Å2 / ksol: 0.267 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
14.8786 Å2
-0 Å2
9.652 Å2
2-
-
-27.5348 Å2
-0 Å2
3-
-
-
13.1256 Å2
Refinement step
Cycle: LAST / Resolution: 2.9→43.437 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11736
0
42
56
11834
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
12105
X-RAY DIFFRACTION
f_angle_d
0.807
16359
X-RAY DIFFRACTION
f_dihedral_angle_d
14.572
4482
X-RAY DIFFRACTION
f_chiral_restr
0.055
1743
X-RAY DIFFRACTION
f_plane_restr
0.003
2133
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.9-3.0037
0.4689
110
0.3595
1944
X-RAY DIFFRACTION
46
3.0037-3.1239
0.4064
128
0.301
2699
X-RAY DIFFRACTION
64
3.1239-3.266
0.354
189
0.292
3434
X-RAY DIFFRACTION
81
3.266-3.4381
0.3546
225
0.2855
3867
X-RAY DIFFRACTION
92
3.4381-3.6534
0.3234
225
0.2637
4135
X-RAY DIFFRACTION
98
3.6534-3.9354
0.3237
215
0.2352
4224
X-RAY DIFFRACTION
100
3.9354-4.3311
0.2749
224
0.2012
4210
X-RAY DIFFRACTION
100
4.3311-4.957
0.2393
229
0.174
4223
X-RAY DIFFRACTION
100
4.957-6.2424
0.2687
235
0.19
4234
X-RAY DIFFRACTION
100
6.2424-43.4417
0.249
211
0.209
4255
X-RAY DIFFRACTION
99
+
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