Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.32 Å3/Da / Density % sol: 47 %
Resolution: 1.7→29.161 Å / Num. obs: 28153 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 17.089 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 7
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
1.7-1.74
4.1
0.636
1.2
8335
2052
0.636
100
1.74-1.79
4.1
0.507
1.5
8106
1992
0.507
100
1.79-1.84
4.1
0.397
2
7953
1956
0.397
100
1.84-1.9
4.1
0.331
2.4
7661
1879
0.331
100
1.9-1.96
4.1
0.255
3
7584
1861
0.255
100
1.96-2.03
4.1
0.211
3.7
7227
1774
0.211
100
2.03-2.11
4.1
0.171
4.5
7003
1716
0.171
100
2.11-2.19
4.1
0.144
5.3
6766
1659
0.144
100
2.19-2.29
4.1
0.12
6.3
6480
1586
0.12
100
2.29-2.4
4.1
0.111
6.8
6271
1534
0.111
100
2.4-2.53
4.1
0.107
6.9
5924
1455
0.107
100
2.53-2.69
4.1
0.095
7.7
5560
1358
0.095
100
2.69-2.87
4.1
0.087
8.2
5366
1321
0.087
100
2.87-3.1
4
0.072
9.7
4876
1204
0.072
100
3.1-3.4
4
0.057
11.4
4511
1124
0.057
100
3.4-3.8
4
0.049
13.3
4050
1013
0.049
100
3.8-4.39
3.9
0.044
13.7
3588
909
0.044
100
4.39-5.38
3.9
0.04
14.7
3035
782
0.04
100
5.38-7.6
3.8
0.044
14.7
2375
618
0.044
100
7.6-29.161
3.5
0.032
18.3
1260
360
0.032
98.3
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0067
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: 1.7→29.161 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.029 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / 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. GLYCEROL, PEG AND CALCIUM WERE MODELED BASED ON PURIFICATION, CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. 4. THERE IS UNMODELED DENSITY BETWEEN AMINO ACIDS ASP139 AND ASN141.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.203
1414
5 %
RANDOM
Rwork
0.173
-
-
-
obs
0.174
28130
100 %
-
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: 15.505 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.31 Å2
0 Å2
0 Å2
2-
-
-0.68 Å2
0 Å2
3-
-
-
-0.63 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→29.161 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1823
0
49
193
2065
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1974
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1335
X-RAY DIFFRACTION
r_angle_refined_deg
1.73
1.993
2690
X-RAY DIFFRACTION
r_angle_other_deg
1.186
3
3251
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.256
5
267
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.239
23.194
72
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.943
15
275
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.416
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.098
0.2
300
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
2260
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
391
X-RAY DIFFRACTION
r_mcbond_it
0.941
1.5
1298
X-RAY DIFFRACTION
r_mcbond_other
0.254
1.5
530
X-RAY DIFFRACTION
r_mcangle_it
1.605
2
2072
X-RAY DIFFRACTION
r_scbond_it
2.406
3
676
X-RAY DIFFRACTION
r_scangle_it
3.722
4.5
617
LS refinement shell
Resolution: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.281
100
-
Rwork
0.242
1946
-
all
-
2046
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: -12.1263 Å / Origin y: -44.1296 Å / Origin z: 3.7875 Å
11
12
13
21
22
23
31
32
33
T
-0.017 Å2
0.0149 Å2
0.01 Å2
-
-0.0315 Å2
-0.0094 Å2
-
-
-0.0352 Å2
L
0.7355 °2
0.0484 °2
0.2721 °2
-
0.8839 °2
-0.1065 °2
-
-
0.4209 °2
S
0.0035 Å °
-0.0359 Å °
0.0877 Å °
0.0477 Å °
-0.0166 Å °
0.071 Å °
-0.0879 Å °
-0.0519 Å °
0.0131 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