Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2.6→29.65 Å / Num. all: 26472 / Num. obs: 26251 / % possible obs: 99.2 % / Redundancy: 4.48 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.0465 / Net I/σ(I): 21.28
Reflection shell
Resolution: 2.6→2.65 Å / Redundancy: 1.96 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 1351 / Rsym value: 0.3179 / % possible all: 93.2
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
MOLREP
phasing
REFMAC
refmac_5.2.0005
refinement
PDB_EXTRACT
1.6
dataextraction
PROTEUM PLUS
2
datareduction
SAINT
datascaling
SADABS
datascaling
XPREP
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2TRX_A Resolution: 2.6→29.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.871 / SU B: 11.143 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 1.154 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Xtalview, Molprobity were also used for the refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.276
1328
5.1 %
RANDOM
Rwork
0.203
-
-
-
all
0.207
-
-
-
obs
-
24866
99.16 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 23.307 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.02 Å2
0 Å2
0 Å2
2-
-
-0.21 Å2
0 Å2
3-
-
-
0.24 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→29.65 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5659
0
56
119
5834
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
5884
X-RAY DIFFRACTION
r_angle_refined_deg
1.237
1.989
8007
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.723
5
738
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.157
26.553
235
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.681
15
1013
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.353
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
941
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
4298
X-RAY DIFFRACTION
r_nbd_refined
0.203
0.2
2521
X-RAY DIFFRACTION
r_nbtor_refined
0.298
0.2
3946
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.126
0.2
217
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.207
0.2
76
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.191
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
1.296
2
3824
X-RAY DIFFRACTION
r_mcangle_it
2.001
3
5977
X-RAY DIFFRACTION
r_scbond_it
1.13
2
2336
X-RAY DIFFRACTION
r_scangle_it
1.663
3
2030
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
% reflection obs (%)
2.6-2.667
0.391
87
0.285
1729
0.29
1910
95.079
2.667-2.74
0.358
93
0.267
1754
0.271
1880
98.245
2.74-2.82
0.399
106
0.261
1666
0.269
1802
98.335
2.82-2.906
0.347
88
0.249
1682
0.254
1787
99.049
2.906-3.002
0.306
91
0.227
1617
0.231
1712
99.766
3.002-3.107
0.256
89
0.197
1584
0.2
1673
100
3.107-3.224
0.322
74
0.22
1532
0.225
1606
100
3.224-3.355
0.277
104
0.203
1451
0.209
1555
100
3.355-3.504
0.236
70
0.203
1427
0.205
1497
100
3.504-3.675
0.271
69
0.207
1352
0.21
1421
100
3.675-3.873
0.292
62
0.181
1299
0.185
1361
100
3.873-4.107
0.205
64
0.179
1230
0.181
1294
100
4.107-4.389
0.244
63
0.172
1148
0.175
1211
100
4.389-4.74
0.199
60
0.148
1092
0.151
1152
100
4.74-5.19
0.226
40
0.16
1011
0.163
1051
100
5.19-5.798
0.243
44
0.192
914
0.194
958
100
5.798-6.688
0.321
46
0.222
816
0.227
862
100
6.688-8.173
0.337
37
0.21
693
0.216
730
100
8.173-11.482
0.211
28
0.149
566
0.152
594
100
11.482-29.65
0.308
13
0.282
303
0.284
360
87.778
+
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