BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
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.
Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % Description: THE PHASE RESTRAINTS FROM A DIFFERENT CRYSTAL WERE USED IN THE REFINEMENT OF THIS DATASET.
Resolution: 1.9→28.88 Å / Num. obs: 41676 / % possible obs: 93.6 % / Biso Wilson estimate: 31.858 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.48
Reflection shell
Diffraction-ID: 1,2
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique all
% possible all
1.9-1.97
0.518
2.1
13215
6555
78.9
1.97-2.05
0.41
2.8
15129
7129
86.7
2.05-2.14
0.311
3.8
15122
7046
90.3
2.14-2.25
0.293
4.9
19017
7367
93.2
2.25-2.39
0.242
6.1
21499
7700
95.1
2.39-2.58
0.185
8.3
25727
8070
96.7
2.58-2.84
0.133
10.9
26960
7950
97.7
2.84-3.25
0.088
14.6
26610
7936
98.6
3.25
0.059
21.5
26096
7980
99.4
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHARP
phasing
REFMAC
5.2.0019
refinement
XSCALE
datascaling
PDB_EXTRACT
2
dataextraction
XDS
datareduction
SHELX
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.9→28.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.477 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.129 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. MODELING OF FE IONS IS SUPPORTED BY METAL EXCITATION SCAN. 4. NO3 AND PEG 200 (PG4) MOLECULES FROM THE CRYSTALLIZATION AND CRYO SOLUTIONS (RESPECTIVELY) ARE MODELED. 5. A 2'-DEOXYGUANOSINE 5'-DIPHOSPHATE (DGI) MOLECULE WAS MODELED IN CHAIN B NEAR THE DI-IRON SITE. THE ASSIGNMENT WAS BASED ON THE DENSITY, PFAM ANNOTATION AND SIMILAR STRUCTURES. THE DENSITY IN CHAIN A NEAR THE DI-IRON SITE WAS NOT AS CLEAR AND WAS MODELED AS A PHOSPHATE AND UNKNOWN LIAGND (UNL). 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.223
2112
5.1 %
RANDOM
Rwork
0.174
-
-
-
obs
0.176
41665
98.62 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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