Resolution: 2.09→29.285 Å / Num. obs: 29521 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.93 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.84
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.09-2.16
0.61
2.2
16187
4554
1
83.2
2.16-2.25
0.512
2.8
22998
5888
1
97.8
2.25-2.35
0.422
3.3
21861
5597
1
98.2
2.35-2.48
0.329
4.1
23300
5953
1
97.9
2.48-2.63
0.245
5.3
21407
5471
1
97.7
2.63-2.83
0.169
7.3
21976
5638
1
98.6
2.83-3.12
0.116
9.7
22795
5864
1
98.5
3.12-3.57
0.079
13.8
21973
5702
1
98.9
3.57-4.49
0.059
18.1
21637
5741
1
99.2
4.49-29.285
0.042
20.5
22122
5795
1
98.7
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 2.09→29.285 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.957 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.112 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL MOLECULE FROM CRYOPROTECTANT IS MODELED IN THIS STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.192
1494
5.1 %
RANDOM
Rwork
0.175
-
-
-
obs
0.176
29517
97.42 %
-
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: 31.806 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.05 Å2
1.02 Å2
0 Å2
2-
-
2.05 Å2
0 Å2
3-
-
-
-3.07 Å2
Refinement step
Cycle: LAST / Resolution: 2.09→29.285 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1863
0
6
143
2012
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
1970
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1223
X-RAY DIFFRACTION
r_angle_refined_deg
1.739
1.942
2718
X-RAY DIFFRACTION
r_angle_other_deg
1.095
3
3010
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.397
5
250
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.931
24.5
80
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.662
15
271
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.156
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
314
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2220
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
378
X-RAY DIFFRACTION
r_nbd_refined
0.207
0.3
402
X-RAY DIFFRACTION
r_nbd_other
0.183
0.3
1250
X-RAY DIFFRACTION
r_nbtor_refined
0.182
0.5
961
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.5
919
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.193
0.5
184
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.211
0.3
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.289
0.3
16
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.159
0.5
15
X-RAY DIFFRACTION
r_mcbond_it
2.047
3
1296
X-RAY DIFFRACTION
r_mcbond_other
0.517
3
494
X-RAY DIFFRACTION
r_mcangle_it
3.177
5
2017
X-RAY DIFFRACTION
r_scbond_it
5.049
8
807
X-RAY DIFFRACTION
r_scangle_it
6.191
11
701
LS refinement shell
Resolution: 2.09→2.15 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.294
105
-
Rwork
0.272
1806
-
all
-
1911
-
obs
-
-
86.9 %
Refinement TLS params.
Method: refined / Origin x: 9.242 Å / Origin y: 50.235 Å / Origin z: 7.348 Å
11
12
13
21
22
23
31
32
33
T
-0.1212 Å2
0.0204 Å2
-0.0012 Å2
-
-0.0824 Å2
-0.0136 Å2
-
-
-0.1255 Å2
L
2.0977 °2
-0.686 °2
-0.759 °2
-
1.2413 °2
0.0769 °2
-
-
3.6581 °2
S
0.067 Å °
-0.0265 Å °
0.0592 Å °
0.0401 Å °
-0.04 Å °
-0.0029 Å °
-0.2156 Å °
-0.1226 Å °
-0.0269 Å °
+
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