4WR2
Crystal structure of a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | Protein (18.02 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) was combined with an equal volume of Reservoir (100 mM Sodium Citrate pH 5.5, 40% PEG 600), Cryoprotection (100 mM Sodium Citrate pH 5.5, 40% PEG 600) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.35 | 63.32 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 60.078 | α = 90 |
b = 115.047 | β = 90 |
c = 141.64 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX225HE | MIRRORS | 2013-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.7 | 30 | 99.5 | 0.078 | 0.078 | 8.6 | 7.7 | 104560 | 22.82 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 1.76 | 99.2 | 0.97 | 7.6 | 10451 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.7 | 29.767 | 104560 | 1997 | 99.19 | 0.1572 | 0.1566 | 0.1713 | RANDOM | 31.367 |
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] | |
3.2 | -1.64 | -1.56 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.8 |
r_dihedral_angle_4_deg | 23.519 |
r_sphericity_bonded | 12.078 |
r_dihedral_angle_3_deg | 10.772 |
r_dihedral_angle_1_deg | 7.324 |
r_rigid_bond_restr | 6.133 |
r_angle_other_deg | 1.839 |
r_angle_refined_deg | 1.312 |
r_mcangle_it | 1.189 |
r_mcbond_it | 1.132 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2345 |
Nucleic Acid Atoms | |
Solvent Atoms | 284 |
Heterogen Atoms | 33 |
Software
Software | |
---|---|
Software Name | Purpose |
SCALEPACK | data scaling |
PHENIX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |