3RI6
A Novel Mechanism of Sulfur Transfer Catalyzed by O-Acetylhomoserine Sulfhydrylase in Methionine Biosynthetic Pathway of Wolinella succinogenes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CB1 | PDB ENTRY 2CB1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 295 | 25-30% (w/v) ethylene glycol and 5% (v/v) N-dodecyl-N, N-dimethylamine-N-oxide, pH 8, vapor diffusion, hanging drop, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 161.8 | α = 90 |
b = 62.5 | β = 120.5 |
c = 91.6 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 100 | CCD | ADSC QUANTUM 270 | 2010-03-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | CHESS | F1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.2 | 30 | 96.8 | 0.128 | 6.2 | 2.4 | 39656 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.24 | 98.6 | 0.458 | 2.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2CB1 | 2.2 | 30 | 38264 | 2017 | 98.95 | 0.22615 | 0.22476 | 0.25085 | RANDOM | 23.575 |
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] | |
-2.06 | -1.23 | 1.07 | -0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.481 |
r_dihedral_angle_4_deg | 19.503 |
r_dihedral_angle_3_deg | 17.823 |
r_dihedral_angle_1_deg | 6.283 |
r_scangle_it | 4.755 |
r_scbond_it | 3.015 |
r_angle_refined_deg | 1.942 |
r_mcangle_it | 1.798 |
r_mcbond_it | 0.974 |
r_chiral_restr | 0.147 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5265 |
Nucleic Acid Atoms | |
Solvent Atoms | 183 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CCP4 | phasing |