4YSL
Crystal structure of SdoA from Pseudomonas putida in complex with glutathione
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | 200 mM Ammonium acetate, 100 mM HEPES (pH 7.5), and 25% (w/v) PEG 3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.28 | 46.01 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79.625 | α = 90 |
b = 79.625 | β = 90 |
c = 93.949 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 77 | CCD | ADSC QUANTUM 315r | 2014-01-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.00000 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.46 | 50 | 98.18 | 30.6 | 2.4 | 101163 | 100527 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 1.4618 | 40.459 | 1.33 | 99194 | 1971 | 98.18 | 0.177 | 0.1765 | 0.2037 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.668 |
f_angle_d | 1.546 |
f_chiral_restr | 0.102 |
f_bond_d | 0.014 |
f_plane_restr | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4582 |
Nucleic Acid Atoms | |
Solvent Atoms | 694 |
Heterogen Atoms | 42 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data scaling |
PHENIX | phasing |
Coot | model building |