7BA4
Structure of Cystathionine gamma-lyase from Pseudomonas aeruginosa
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NMP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 291 | 9%PEG 4000 0.1M Sodium acetate pH 4.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.304 | α = 90 |
b = 79.304 | β = 90 |
c = 446.668 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | 195 | PIXEL | PSI PILATUS 6M | 2011-11-24 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.97 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.999 | 148.889 | 99.9 | 0.158 | 0.162 | 0.037 | 0.995 | 13.9 | 18.3 | 112386 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.999 | 2.033 | 98.8 | 0.78 | 0.82 | 0.247 | 0.775 | 10.6 |
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 (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2NMP | 2 | 54.45 | 1.33 | 111968 | 5679 | 99.69 | 0.1619 | 0.1595 | 0.2052 | 40.9117 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11244 |
Nucleic Acid Atoms | |
Solvent Atoms | 1177 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |