2PRX
Crystal structure of Thioesterase superfamily protein (ZP_00837258.1) from Shewanella loihica PV-4 at 1.65 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 277 | NANODROP, 2.4M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | NANODROP, 2.4M (NH4)2SO4, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.501 | α = 90 |
b = 38.501 | β = 90 |
c = 172.247 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
2 | 1 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2007-02-15 | M | MAD | |||||
1 | 2 | CCD | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2007-02-23 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837 | SSRL | BL11-1 |
2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97927, 0.97941, 0.91162 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||
2 | 1.5 | 86.066 | 76.7 | 0.05 | 0.05 | 9.4 | 2.9 | 35176 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2 | 1.5 | 1.54 | 61.3 | 0.183 | 0.183 | 4.1 | 2.7 | 2100 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | FREE R | 1.5 | 28.736 | 35176 | 35102 | 1811 | 72.7 | 0.203 | 0.199 | 0.199 | 0.277 | RANDOM EXPANDED BY TWIN LAW | 15.625 |
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 |
s_similar_adp_cmpnt | 0.065 |
s_similar_dist | 0.064 |
s_zero_chiral_vol | 0.041 |
s_non_zero_chiral_vol | 0.041 |
s_from_restr_planes | 0.027 |
s_angle_d | 0.026 |
s_anti_bump_dis_restr | 0.024 |
s_bond_d | 0.008 |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1705 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
SHELX | refinement |
MolProbity | model building |
SOLVE | phasing |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
SHELXL-97 | refinement |