3M8U
Crystal structure of glutathione-binding protein A (GbpA) from Haemophilus parasuis SH0165 in complex with glutathione disulfide (GSSG)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DPP | PDB ENTRY 1DPP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000 or 4% tacsimate pH4.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.52 | α = 90 |
b = 68.47 | β = 90 |
c = 142.32 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2009-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.9714 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.85 | 40 | 99.9 | 0.086 | 19.9 | 7.29 | 48827 | 48793 | 16.69 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.85 | 1.9 | 99.9 | 0.602 | 3.19 | 7.07 | 3554 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1DPP | 1.85 | 38.995 | 2 | 48827 | 48787 | 2440 | 99.93 | 0.1598 | 0.1598 | 0.1583 | 0.16 | 0.1883 | 0.19 | RANDOM | 20.68 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.043 | 0.399 | -0.442 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.995 |
f_angle_d | 0.991 |
f_chiral_restr | 0.066 |
f_plane_restr | 0.011 |
f_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4026 |
Nucleic Acid Atoms | |
Solvent Atoms | 594 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |