5B36
Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with Cysteine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3VSA | CysO free form (PDB ID, 3VSA) |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 296 | 0.1 M HEPES sodium pH 7.5, 27% 2-propanol, 10% PEG4000, 12 mM TCEP-HCl, the crystal was soaked with the reservoir solution containing 6% MPD as a cryoprotectant, 20 mM L-cysteine, and 12 mM TCEP-HCl |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.29 | 46.24 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 74.181 | α = 90 |
b = 74.181 | β = 90 |
c = 278.994 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 80 | CCD | Bruker DIP-6040 | 2010-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
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 | 2.15 | 49.1 | 92 | 17 | 13.5 | 43621 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.14 | 2.18 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | FOURIER SYNTHESIS | THROUGHOUT | CysO free form (PDB ID, 3VSA) | 2.15 | 49.1 | 38060 | 1991 | 92.11 | 0.18335 | 0.18017 | 0.24598 | RANDOM | 36.235 |
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] | |
0.21 | 0.21 | -0.43 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.594 |
r_dihedral_angle_4_deg | 18.286 |
r_dihedral_angle_3_deg | 17.386 |
r_dihedral_angle_1_deg | 6.938 |
r_scangle_it | 5.338 |
r_scbond_it | 3.409 |
r_angle_refined_deg | 2.091 |
r_mcangle_it | 2.077 |
r_mcbond_it | 1.168 |
r_chiral_restr | 0.223 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5834 |
Nucleic Acid Atoms | |
Solvent Atoms | 268 |
Heterogen Atoms | 52 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |