- PDB-3gv1: Crystal structure of disulfide interchange protein from Neisseria... -
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Basic information
Entry
Database: PDB / ID: 3gv1
Title
Crystal structure of disulfide interchange protein from Neisseria gonorrhoeae
Components
Disulfide interchange protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / disulfide interchange protein / Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) / DsbC / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Resolution: 2→2.11 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3671 / % possible all: 95.5
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Processing
Software
Name
Version
Classification
CBASS
datacollection
PHENIX
AUTOSOL
modelbuilding
PHENIX
refinement
MOSFLM
datareduction
SCALA
datascaling
PHENIX
AUTOSOL
phasing
Refinement
Method to determine structure: SAD / Resolution: 2→26.04 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.228
1314
5.06 %
random
Rwork
0.1797
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-
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obs
0.1822
25977
98.07 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.67 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Biso mean: 24.05 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.8338 Å2
0 Å2
-0.0732 Å2
2-
-
5.1229 Å2
0 Å2
3-
-
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-10.9567 Å2
Refinement step
Cycle: LAST / Resolution: 2→26.04 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3298
0
27
180
3505
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
% reflection obs (%)
2-2.0801
0.3054
141
0.225
2618
94
2.0801-2.1747
0.2784
128
0.1968
2751
98
2.1747-2.2893
0.2851
163
0.1883
2718
98
2.2893-2.4326
0.2461
135
0.1798
2736
99
2.4326-2.6203
0.265
128
0.1755
2772
99
2.6203-2.8836
0.2429
148
0.1888
2759
99
2.8836-3.3002
0.2087
150
0.1701
2747
99
3.3002-4.1552
0.1762
156
0.1565
2787
99
4.1552-26.0423
0.2144
165
0.1804
2775
98
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