Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 80 TO MET ...ENGINEERED RESIDUE IN CHAIN A, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 80 TO MET
Nonpolymer details
PEG 400 (PG4): PEG 3350 IN CRYSTALLISATION CONDITIONS MODELLED AS PEG 400
-
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 % / Description: RD1, RD2 USED AS SEPARATE SEARCH MODELS
Resolution: 2.89→47.14 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 30.39 / Stereochemistry target values: ML Details: FOR ALL CHAINS IN THE ASYMMETRIC UNIT ELECTRON DENSITY FOR AMINO ACIDS ALA 201 TO VAL 209 IS DISORDERED. THE MODEL IN THESE REGIONS SHOULD BE TREATED WITH CAUTION.
Rfactor
Num. reflection
% reflection
Rfree
0.287
1057
5.2 %
Rwork
0.242
-
-
obs
0.244
20450
93.7 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.22 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Biso mean: 32.3 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.2822 Å2
0 Å2
4.5373 Å2
2-
-
-5.3834 Å2
0 Å2
3-
-
-
0.1011 Å2
Refinement step
Cycle: LAST / Resolution: 2.89→47.14 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6380
0
69
53
6502
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
6625
X-RAY DIFFRACTION
f_angle_d
1.409
8995
X-RAY DIFFRACTION
f_dihedral_angle_d
17.582
2364
X-RAY DIFFRACTION
f_chiral_restr
0.087
1008
X-RAY DIFFRACTION
f_plane_restr
0.006
1158
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
1436
X-RAY DIFFRACTION
POSITIONAL
1
2
B
1436
X-RAY DIFFRACTION
POSITIONAL
0.066
1
3
C
1446
X-RAY DIFFRACTION
POSITIONAL
0.049
1
4
D
1421
X-RAY DIFFRACTION
POSITIONAL
0.071
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8854-3.0167
0.368
127
0.308
2240
X-RAY DIFFRACTION
87
3.0167-3.1757
0.3869
144
0.295
2397
X-RAY DIFFRACTION
94
3.1757-3.3746
0.331
127
0.2687
2449
X-RAY DIFFRACTION
94
3.3746-3.6351
0.2747
119
0.2366
2449
X-RAY DIFFRACTION
94
3.6351-4.0007
0.2498
138
0.2225
2430
X-RAY DIFFRACTION
95
4.0007-4.5792
0.2739
121
0.2081
2467
X-RAY DIFFRACTION
95
4.5792-5.7677
0.231
145
0.2041
2470
X-RAY DIFFRACTION
95
5.7677-47.1495
0.2617
136
0.2309
2491
X-RAY DIFFRACTION
95
+
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