- PDB-3hg7: CRYSTAL STRUCTURE OF D-isomer specific 2-hydroxyacid dehydrogenas... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3hg7
Title
CRYSTAL STRUCTURE OF D-isomer specific 2-hydroxyacid dehydrogenase family protein from Aeromonas salmonicida subsp. salmonicida A449
Components
D-isomer specific 2-hydroxyacid dehydrogenase family protein
Keywords
OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / D-isomer specific 2-hydroxyacid dehydrogenase / PSI-2 / New York SGX Research Center for Structural Genomics
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9791 Å / Relative weight: 1
Reflection
Redundancy: 7.2 % / Av σ(I) over netI: 36.23 / Number: 569940 / Rmerge(I) obs: 0.062 / Χ2: 1.23 / D res high: 1.79 Å / D res low: 50 Å / Num. obs: 78686 / % possible obs: 98
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.86
50
98.5
1
0.027
1.697
7.7
3.86
4.86
100
1
0.032
1.838
7.4
3.37
3.86
100
1
0.05
2.788
7.6
3.06
3.37
100
1
0.053
1.95
7.7
2.84
3.06
100
1
0.053
1.306
7.7
2.67
2.84
100
1
0.062
1.129
7.7
2.54
2.67
100
1
0.077
1.069
7.7
2.43
2.54
100
1
0.093
1.038
7.7
2.34
2.43
100
1
0.113
1.008
7.7
2.26
2.34
100
1
0.129
1.004
7.7
2.18
2.26
100
1
0.162
1.013
7.6
2.12
2.18
100
1
0.211
0.989
7.6
2.07
2.12
100
1
0.246
0.959
7.6
2.02
2.07
100
1
0.294
0.961
7.6
1.97
2.02
100
1
0.387
0.948
7.5
1.93
1.97
99.8
1
0.462
0.937
7.3
1.89
1.93
99.1
1
0.55
0.914
6.9
1.85
1.89
96.5
1
0.659
0.873
6.2
1.82
1.85
91.8
1
0.812
0.873
5.2
1.79
1.82
74.7
1
0.809
0.83
3.9
Reflection
Resolution: 1.79→50 Å / Num. obs: 78686 / % possible obs: 98 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.062 / Χ2: 1.233 / Net I/σ(I): 36.234
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.79-1.82
3.9
0.809
3008
0.83
1
74.7
1.82-1.85
5.2
0.812
3671
0.873
1
91.8
1.85-1.89
6.2
0.659
3872
0.873
1
96.5
1.89-1.93
6.9
0.55
3954
0.914
1
99.1
1.93-1.97
7.3
0.462
4017
0.937
1
99.8
1.97-2.02
7.5
0.387
4046
0.948
1
100
2.02-2.07
7.6
0.294
3987
0.961
1
100
2.07-2.12
7.6
0.246
4016
0.959
1
100
2.12-2.18
7.6
0.211
4006
0.989
1
100
2.18-2.26
7.6
0.162
4000
1.013
1
100
2.26-2.34
7.7
0.129
4012
1.004
1
100
2.34-2.43
7.7
0.113
4018
1.008
1
100
2.43-2.54
7.7
0.093
3999
1.038
1
100
2.54-2.67
7.7
0.077
4040
1.069
1
100
2.67-2.84
7.7
0.062
3996
1.129
1
100
2.84-3.06
7.7
0.053
4044
1.306
1
100
3.06-3.37
7.7
0.053
3988
1.95
1
100
3.37-3.86
7.6
0.05
4008
2.788
1
100
3.86-4.86
7.4
0.032
4029
1.838
1
100
4.86-50
7.7
0.027
3975
1.697
1
98.5
-
Phasing
Phasing
Method: molecular replacement
Phasing MR
Rfactor: 38.02 / Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
2.5 Å
32.08 Å
Translation
2.5 Å
32.08 Å
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
2.1.2
phasing
REFMAC
5.5.0070
refinement
PDB_EXTRACT
3.005
dataextraction
CBASS
datacollection
HKL-2000
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.643 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.264
2094
5 %
RANDOM
Rwork
0.228
-
-
-
obs
0.229
41494
99.06 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 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