SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
Resolution: 1.59→26.997 Å / Num. obs: 24172 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 24.182 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 5.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.59-1.63
6.7
0.832
0.9
11754
1753
0.832
100
1.63-1.68
7.3
0.661
1.2
12547
1729
0.661
99.9
1.68-1.72
7.2
0.512
1.5
12001
1664
0.512
100
1.72-1.78
7.3
0.4
1.9
11747
1619
0.4
100
1.78-1.84
7.2
0.296
2.6
11209
1549
0.296
100
1.84-1.9
7.2
0.214
3.5
11037
1525
0.214
100
1.9-1.97
7.3
0.171
4.3
10736
1479
0.171
100
1.97-2.05
7.2
0.133
5.4
10244
1414
0.133
100
2.05-2.14
7.2
0.113
6.2
9854
1361
0.113
100
2.14-2.25
7.2
0.098
7.1
9469
1312
0.098
100
2.25-2.37
7.2
0.084
8
9034
1251
0.084
100
2.37-2.51
7.2
0.077
8.4
8603
1188
0.077
100
2.51-2.69
7.2
0.075
8.5
8037
1120
0.075
100
2.69-2.9
7.1
0.069
9.3
7450
1045
0.069
100
2.9-3.18
7.1
0.06
10.2
6834
960
0.06
100
3.18-3.56
7
0.052
11.8
6187
882
0.052
100
3.56-4.11
7
0.053
11.4
5501
789
0.053
100
4.11-5.03
6.8
0.047
13.3
4582
673
0.047
100
5.03-7.11
6.6
0.043
13.7
3582
543
0.043
100
7.11-26.997
5.9
0.039
15
1869
316
0.039
97.8
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.59→26.997 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.75 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.099 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. UNKNOWN LIGAND (UNL) WAS MODELED BASED ON RELATED STRUCTURES.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.252
1232
5.1 %
RANDOM
Rwork
0.203
-
-
-
obs
0.206
24135
99.96 %
-
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: 19.654 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.27 Å2
0.13 Å2
0 Å2
2-
-
0.27 Å2
0 Å2
3-
-
-
-0.4 Å2
Refinement step
Cycle: LAST / Resolution: 1.59→26.997 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1160
0
11
107
1278
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1268
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
827
X-RAY DIFFRACTION
r_angle_refined_deg
1.654
1.96
1750
X-RAY DIFFRACTION
r_angle_other_deg
0.961
3
2052
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.149
5
171
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.651
25.088
57
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.594
15
223
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.551
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.111
0.2
210
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1421
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
249
X-RAY DIFFRACTION
r_nbd_refined
0.245
0.2
233
X-RAY DIFFRACTION
r_nbd_other
0.204
0.2
827
X-RAY DIFFRACTION
r_nbtor_refined
0.185
0.2
620
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.2
703
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.172
0.2
87
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.258
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.272
0.2
54
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.112
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
1.294
1.5
838
X-RAY DIFFRACTION
r_mcbond_other
0.315
1.5
304
X-RAY DIFFRACTION
r_mcangle_it
1.836
2
1276
X-RAY DIFFRACTION
r_scbond_it
2.546
3
543
X-RAY DIFFRACTION
r_scangle_it
3.598
4.5
461
LS refinement shell
Resolution: 1.59→1.631 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.311
76
-
Rwork
0.296
1669
-
obs
-
1745
99.94 %
Refinement TLS params.
Method: refined / Origin x: 11.028 Å / Origin y: 41.305 Å / Origin z: 0.987 Å
11
12
13
21
22
23
31
32
33
T
-0.0469 Å2
0.0198 Å2
0.0291 Å2
-
-0.0695 Å2
0.001 Å2
-
-
-0.0573 Å2
L
2.3041 °2
-0.8257 °2
-0.4616 °2
-
1.2989 °2
-0.262 °2
-
-
1.4517 °2
S
-0.0684 Å °
-0.0392 Å °
-0.0959 Å °
0.1387 Å °
0.0944 Å °
0.1316 Å °
-0.1722 Å °
-0.0265 Å °
-0.026 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