Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9791831 Å / Relative weight: 1
Reflection
Resolution: 1.648→50 Å / Num. all: 20664 / Num. obs: 19834 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 28.4
Reflection shell
Resolution: 1.65→1.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.2 / Num. unique all: 995 / % possible all: 99.5
-
Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
SHELX
modelbuilding
MLPHARE
phasing
DM
modelbuilding
ARP/wARP
modelbuilding
Coot
modelbuilding
PHENIX
(phenix.refine: 1.6.1_357)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
SHELX
phasing
DM
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.648→25.687 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1833
1007
5.08 %
random
Rwork
0.1596
-
-
-
all
0.1608
20835
-
-
obs
0.1608
19828
98.71 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.393 Å2 / ksol: 0.424 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-0.9674 Å2
-0 Å2
0 Å2
2-
-
-0.9674 Å2
-0 Å2
3-
-
-
1.9347 Å2
Refinement step
Cycle: LAST / Resolution: 1.648→25.687 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1094
0
51
84
1229
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
1208
X-RAY DIFFRACTION
f_angle_d
1.298
1634
X-RAY DIFFRACTION
f_dihedral_angle_d
12.517
475
X-RAY DIFFRACTION
f_chiral_restr
0.082
180
X-RAY DIFFRACTION
f_plane_restr
0.005
205
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.6476-1.7344
0.2381
149
0.2119
2645
X-RAY DIFFRACTION
99
1.7344-1.8431
0.2035
174
0.1828
2695
X-RAY DIFFRACTION
100
1.8431-1.9853
0.1879
151
0.158
2658
X-RAY DIFFRACTION
99
1.9853-2.185
0.1897
137
0.1435
2696
X-RAY DIFFRACTION
100
2.185-2.5009
0.1778
133
0.1378
2697
X-RAY DIFFRACTION
99
2.5009-3.15
0.186
131
0.1506
2706
X-RAY DIFFRACTION
98
3.15-25.6898
0.1637
132
0.1633
2724
X-RAY DIFFRACTION
96
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.9635
-0.2213
0.3602
1.3551
-0.0629
0.1447
0.0596
-0.3254
-0.0113
0.2839
0.0447
-0.0813
-0.0248
-0.0065
-0.0578
0.176
-0.023
-0.0229
0.1587
0.0239
0.1401
36.7684
59.6621
9.9276
2
1.3692
1.0001
-0.067
1.3476
-0.6398
1.4426
0.016
0.002
-0.0835
0.0999
0.0042
-0.1089
0.1148
-0.0103
-0.015
0.1983
-0.0534
-0.0369
0.116
0.0351
0.1923
30.8229
46.9099
3.2243
3
1.7539
0.8078
0.6791
1.7427
0.4902
2.4144
-0.3952
-0.0563
0.035
-0.2949
-0.025
0.063
0.14
-0.2266
0.2667
0.2299
-0.0633
-0.0482
0.1045
0.0369
0.1882
26.4493
42.9259
0.2233
4
0.6333
0.0858
0.175
1.4044
-1.0196
0.868
0.0679
0.2261
-0.0995
-0.5844
0.0572
0.0963
0.2779
-0.0015
-0.0972
0.2387
-0.0378
-0.0691
0.113
0.0173
0.1892
27.7208
53.0837
-5.9858
5
1.1953
-0.933
1.0285
2.8069
-1.7156
1.551
0.211
0.2136
0.0322
-0.6784
-0.0554
0.2121
0.0831
0.0856
-0.1136
0.2352
0.0054
-0.0816
0.1465
0.0117
0.1569
29.6076
59.7187
-7.8636
6
0.4737
0.3691
0.2945
0.5406
0.7546
1.5126
-0.0054
0.0238
-0.0207
-0.0156
0.1255
-0.056
-0.0871
0.1943
-0.1271
0.1227
-0.0038
-0.0135
0.1299
-0.0031
0.1387
46.5842
64.9352
5.688
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid1:15)
2
X-RAY DIFFRACTION
2
(chainAandresid16:57)
3
X-RAY DIFFRACTION
3
(chainAandresid58:71)
4
X-RAY DIFFRACTION
4
(chainAandresid72:90)
5
X-RAY DIFFRACTION
5
(chainAandresid91:118)
6
X-RAY DIFFRACTION
6
(chainAandresid119:138)
+
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