Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97951 Å / Relative weight: 1
Reflection twin
Type
Crystal-ID
ID
Operator
Domain-ID
Fraction
pseudo-merohedral
1
1
H, K, L
1
0.696
pseudo-merohedral
2
2
-h,-k,l
2
0.304
Reflection
Resolution: 1.88→59.96 Å / Num. obs: 20355 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8
Reflection shell
Resolution: 1.88→1.92 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1034 / CC1/2: 0.839 / % possible all: 96.3
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
XDS
datareduction
Aimless
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house model Resolution: 1.881→59.957 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.996 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.032 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.222
1071
5.262 %
Rwork
0.177
19283
-
all
0.179
-
-
obs
-
20354
95.775 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parameters
Biso mean: 34.513 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-15.037 Å2
-0 Å2
-4.747 Å2
2-
-
7.438 Å2
0 Å2
3-
-
-
7.599 Å2
Refinement step
Cycle: LAST / Resolution: 1.881→59.957 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2096
0
130
208
2434
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.013
2305
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.017
2180
X-RAY DIFFRACTION
r_angle_refined_deg
1.308
1.661
3135
X-RAY DIFFRACTION
r_angle_other_deg
1.133
1.661
5039
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.809
5
252
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.818
25
112
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.277
15
385
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.478
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.058
0.2
281
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2540
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
518
X-RAY DIFFRACTION
r_nbd_refined
0.193
0.2
508
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.176
0.2
1975
X-RAY DIFFRACTION
r_nbtor_refined
0.17
0.2
1083
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.08
0.2
927
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.172
0.2
137
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.207
0.2
23
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
109
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.154
0.2
12
X-RAY DIFFRACTION
r_mcbond_it
2.675
4.372
1011
X-RAY DIFFRACTION
r_mcbond_other
2.659
4.37
1010
X-RAY DIFFRACTION
r_mcangle_it
3.771
9.821
1262
X-RAY DIFFRACTION
r_mcangle_other
3.77
9.827
1263
X-RAY DIFFRACTION
r_scbond_it
3.133
5.1
1294
X-RAY DIFFRACTION
r_scbond_other
3.132
5.1
1295
X-RAY DIFFRACTION
r_scangle_it
4.798
11.147
1873
X-RAY DIFFRACTION
r_scangle_other
4.797
11.146
1874
X-RAY DIFFRACTION
r_lrange_it
7.274
40.762
2754
X-RAY DIFFRACTION
r_lrange_other
7.273
40.765
2755
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.881-1.93
0.272
88
0.214
1313
X-RAY DIFFRACTION
89.578
1.93-1.982
0.249
112
0.21
1352
X-RAY DIFFRACTION
96.5699
1.982-2.04
0.274
78
0.202
1352
X-RAY DIFFRACTION
96.8179
2.04-2.103
0.21
57
0.198
1357
X-RAY DIFFRACTION
97.249
2.103-2.171
0.264
94
0.234
1218
X-RAY DIFFRACTION
97.3294
2.171-2.248
0.273
53
0.207
1208
X-RAY DIFFRACTION
92.381
2.248-2.332
0.292
51
0.201
1101
X-RAY DIFFRACTION
88.1408
2.332-2.427
0.307
69
0.209
1138
X-RAY DIFFRACTION
97.2603
2.427-2.535
0.249
53
0.228
1132
X-RAY DIFFRACTION
98.4219
2.535-2.659
0.269
54
0.201
1088
X-RAY DIFFRACTION
97.6068
2.659-2.802
0.157
60
1008
X-RAY DIFFRACTION
96.7391
2.802-2.972
0.258
40
0.19
960
X-RAY DIFFRACTION
97.2763
2.972-3.176
0.272
41
0.185
920
X-RAY DIFFRACTION
97.3658
3.176-3.43
0.231
70
0.173
818
X-RAY DIFFRACTION
97.6898
3.43-3.756
0.145
40
780
X-RAY DIFFRACTION
96.3572
3.756-4.197
0.184
32
0.126
701
X-RAY DIFFRACTION
97.344
4.197-4.843
0.157
39
0.119
618
X-RAY DIFFRACTION
97.1893
4.843-5.922
0.208
20
0.163
540
X-RAY DIFFRACTION
97.3913
5.922-8.334
0.246
8
0.175
440
X-RAY DIFFRACTION
97.6035
8-10
0.238
12
0.165
239
X-RAY DIFFRACTION
95.0758
+
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