Resolution: 1.35→1.42 Å / Rsym value: 0.379 / % possible all: 99
-
Processing
Software
Name
Version
Classification
MxCuBE
datacollection
SHARP
phasing
REFMAC
5.8.0069
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MIR / Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.329 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.05 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18501
5666
5 %
RANDOM
Rwork
0.17248
-
-
-
all
0.1731
107565
-
-
obs
0.1731
107565
99.51 %
-
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: 10.135 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.48 Å2
0 Å2
-0 Å2
2-
-
0.06 Å2
0 Å2
3-
-
-
0.42 Å2
Refinement step
Cycle: LAST / Resolution: 1.35→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3549
0
96
384
4029
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.019
3717
X-RAY DIFFRACTION
r_angle_refined_deg
1.103
1.961
5046
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.887
5
471
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.751
26.053
152
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.396
15
583
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.58
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
580
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
2766
X-RAY DIFFRACTION
r_mcbond_it
0.261
0.622
1890
X-RAY DIFFRACTION
r_mcangle_it
0.471
0.931
2359
X-RAY DIFFRACTION
r_scbond_it
0.367
0.682
1827
X-RAY DIFFRACTION
r_long_range_B_refined
2.968
5.96
6180
LS refinement shell
Resolution: 1.35→1.385 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.208
413
-
Rwork
0.198
7847
-
obs
-
-
99.35 %
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
0.6181
0.0235
-0.0266
0.3632
0.0946
0.5033
-0.005
-0.1043
0.0202
0.0221
0.0155
-0.013
-0.0031
0.0016
-0.0105
0.0158
0.0053
-0.001
0.0206
-0.0064
0.006
6.4243
36.9376
112.8772
2
0.4178
0.0093
-0.0595
0.3521
0.0626
0.3487
0.0016
0.0198
0.0228
-0.0267
0.0045
0
-0.0206
0.005
-0.0061
0.025
-0.0018
-0.0028
0.0014
-0.0008
0.0222
8.853
36.546
84.5447
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 503
2
X-RAY DIFFRACTION
2
B
1 - 506
+
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