Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97887 Å / Relative weight: 1
Reflection
Resolution: 1.7→44.59 Å / Num. obs: 26387 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rrim(I) all: 0.082 / Net I/σ(I): 15.76
Reflection shell
Resolution: 1.7→1.75 Å / Mean I/σ(I) obs: 2.42 / Num. unique obs: 2026 / CC1/2: 0.752 / Rrim(I) all: 0.742
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house model Resolution: 1.7→44.588 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.038 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.087 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1736
884
3.35 %
Rwork
0.1539
25502
-
all
0.155
-
-
obs
-
26386
99.334 %
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: 29.097 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.006 Å2
0 Å2
0 Å2
2-
-
-0.189 Å2
0 Å2
3-
-
-
-0.816 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→44.588 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1875
0
58
179
2112
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.013
2045
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.015
1857
X-RAY DIFFRACTION
r_angle_refined_deg
1.539
1.667
2786
X-RAY DIFFRACTION
r_angle_other_deg
1.429
1.593
4295
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.407
5
253
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.452
22.979
94
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.016
15
333
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.833
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.07
0.2
258
X-RAY DIFFRACTION
r_chiral_restr_other
0.044
0.2
2
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
2331
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
462
X-RAY DIFFRACTION
r_nbd_refined
0.2
0.2
373
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.188
0.2
1815
X-RAY DIFFRACTION
r_nbtor_refined
0.17
0.2
963
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.077
0.2
912
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.153
0.2
138
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.273
0.2
14
X-RAY DIFFRACTION
r_nbd_other
0.189
0.2
47
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.168
0.2
13
X-RAY DIFFRACTION
r_mcbond_it
1.192
2.157
985
X-RAY DIFFRACTION
r_mcbond_other
1.183
2.155
984
X-RAY DIFFRACTION
r_mcangle_it
1.83
3.231
1244
X-RAY DIFFRACTION
r_mcangle_other
1.829
3.233
1245
X-RAY DIFFRACTION
r_scbond_it
1.921
2.545
1060
X-RAY DIFFRACTION
r_scbond_other
1.92
2.547
1061
X-RAY DIFFRACTION
r_scangle_it
3.031
3.69
1541
X-RAY DIFFRACTION
r_scangle_other
3.03
3.692
1542
X-RAY DIFFRACTION
r_lrange_it
5.568
26.933
2323
X-RAY DIFFRACTION
r_lrange_other
5.436
26.306
2285
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.7-1.744
0.262
60
0.238
1732
0.239
1923
0.85
0.851
93.1877
0.218
1.744-1.792
0.292
62
0.209
1786
0.212
1883
0.878
0.904
98.1413
0.181
1.792-1.844
0.222
61
0.184
1755
0.185
1817
0.925
0.936
99.945
0.155
1.844-1.9
0.19
60
0.172
1736
0.173
1797
0.951
0.951
99.9444
0.143
1.9-1.963
0.2
58
0.16
1661
0.161
1720
0.941
0.955
99.9419
0.136
1.963-2.031
0.192
56
0.153
1623
0.154
1680
0.952
0.961
99.9405
0.131
2.031-2.108
0.162
54
0.144
1563
0.145
1617
0.975
0.968
100
0.127
2.108-2.194
0.185
52
0.138
1514
0.139
1566
0.965
0.972
100
0.121
2.194-2.291
0.153
50
0.144
1446
0.144
1496
0.971
0.97
100
0.131
2.291-2.402
0.168
49
0.144
1387
0.145
1437
0.965
0.967
99.9304
0.131
2.402-2.532
0.191
45
0.144
1312
0.145
1357
0.961
0.967
100
0.135
2.532-2.685
0.163
44
0.144
1266
0.144
1310
0.973
0.973
100
0.138
2.685-2.87
0.154
41
0.146
1187
0.146
1228
0.97
0.973
100
0.143
2.87-3.099
0.169
38
0.145
1113
0.145
1151
0.955
0.973
100
0.147
3.099-3.393
0.155
35
0.129
1011
0.13
1046
0.971
0.979
100
0.14
3.393-3.79
0.134
33
0.138
942
0.138
975
0.98
0.976
100
0.153
3.79-4.371
0.128
29
0.145
829
0.145
860
0.978
0.975
99.7674
0.171
4.371-5.341
0.199
25
0.139
722
0.14
748
0.966
0.979
99.8663
0.168
5.341-7.5
0.228
20
0.212
573
0.212
593
0.96
0.957
100
0.239
7.5-44.588
0.147
12
0.22
344
0.217
359
0.966
0.95
99.1643
0.276
Refinement TLS params.
Method: refined / Origin x: -16.6774 Å / Origin y: 9.3566 Å / Origin z: -12.9215 Å
11
12
13
21
22
23
31
32
33
T
0.0097 Å2
-0.0074 Å2
0.0087 Å2
-
0.0164 Å2
-0.0075 Å2
-
-
0.0336 Å2
L
1.753 °2
-0.1933 °2
0.2981 °2
-
1.3853 °2
0.203 °2
-
-
0.7542 °2
S
0.0048 Å °
0.1007 Å °
0.0185 Å °
-0.0973 Å °
0.0347 Å °
-0.0523 Å °
-0.0367 Å °
0.0751 Å °
-0.0395 Å °
Refinement TLS group
Selection: 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