Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2010 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97945 Å / Relative weight: 1
Reflection
Resolution: 1.6→29.452 Å / Num. all: 23715 / Num. obs: 23715 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.737 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.1
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
1.6-1.64
7
0.651
2.7
12174
1743
0.651
100
1.64-1.69
7.1
0.578
3
11918
1680
0.578
100
1.69-1.74
7.2
0.47
3.6
11953
1663
0.47
100
1.74-1.79
7.2
0.383
4.3
11744
1626
0.383
100
1.79-1.85
7.3
0.318
5
11284
1556
0.318
100
1.85-1.91
7.3
0.276
5.8
10961
1506
0.276
100
1.91-1.98
7.2
0.2
7.4
10592
1465
0.2
100
1.98-2.07
7.3
0.163
9.2
10117
1384
0.163
100
2.07-2.16
7.3
0.155
10.8
9940
1357
0.155
100
2.16-2.26
7.3
0.141
12.1
9487
1302
0.141
100
2.26-2.39
7.4
0.124
13.7
8918
1204
0.124
100
2.39-2.53
7.4
0.121
14.2
8677
1175
0.121
100
2.53-2.7
7.4
0.107
15.8
8043
1089
0.107
100
2.7-2.92
7.4
0.087
18.2
7574
1020
0.087
100
2.92-3.2
7.4
0.067
20.7
6953
934
0.067
100
3.2-3.58
7.4
0.057
25.6
6232
841
0.057
100
3.58-4.13
7.4
0.058
28.4
5616
758
0.058
100
4.13-5.06
7.4
0.051
29.2
4739
639
0.051
100
5.06-7.16
7.3
0.061
24.9
3628
495
0.061
100
7.16-29.452
7.1
0.058
26.3
1963
278
0.058
97.9
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
SCALA
3.3.15
datascaling
REFMAC
5.7.0032
refinement
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.6→29.452 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.062 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. A NICKEL ION (NI+2) IS MODELED BASED ON A PEAK IN THE ANOMALOUS DIFFERENCE FOURIER. X-RAY FLUORESCENCE EMISSION SPECTRA SHOWED PEAKS CORRESPONDING TO THE NICKEL AND ZINC K-EDGES. DATA SETS WERE COLLECTED ABOVE AND BELOW THE ZINC AND NICKEL K-EDGES. COMPARING ANOMALOUS DIFFERENCE FOURIER MAPS FROM THESE 4 DATA SETS SUGGESTS A MIXTURE WITH MORE NICKEL THAN ZINC. 7. THE MODELED PEG 200 FRAGMENTS (1PE AND PGE) AND SODIUM IONS ARE PRESENT IN THE CRYSTALLIZATION SOLUTION AND PROTEIN BUFFER. 8. THE SCATTERING FACTORS FOR SULFUR, SELENIUM AND ZINC ATOMS WERE ADJUSTED BY REFMAC 5.7.0032 TO ACCOUNT FOR ANOMALOUS DISPERSION. THE SELENIUM CORRECTION WAS DERIVED FROM THE X-RAY FLUORESCENCE MAD SCAN WITH CHOOCH. THE CORRECTIONS FOR NICKEL AND SULFUR WERE BASED ON THE WAVELENGTH 0.97945 A (S F'= 0.18, SE F'= -7.60, NI F'= 0.06). THE CROMER MANN VALUES LISTED IN THE CIF VERSION OF THE FILE INCLUDE THIS CORRECTION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1808
1222
5.2 %
RANDOM
Rwork
0.1512
-
-
-
obs
0.1526
23680
99.93 %
-
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