2PQ7
Crystal structure of predicted HD superfamily hydrolase (104161995) from uncultured Thermotogales bacterium at 1.45 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 277 | NANODROP, 24.0% 2-methyl-2,4-pentanediol, 0.2M Sodium chloride, 0.1M Sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 138.518 | α = 90 |
b = 40.662 | β = 95.32 |
c = 37.789 | 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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2007-04-14 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837, 0.97916, 0.97867 | SSRL | BL11-1 |
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 | |||||||
1 | 1.45 | 27.441 | 99.9 | 0.065 | 0.065 | 7.2 | 3.7 | 37299 | 17.32 |
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) | ||||||||||
1.45 | 1.49 | 99.8 | 0.701 | 0.701 | 1.1 | 3.7 | 2695 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 1.45 | 27.441 | 37299 | 1864 | 99.85 | 0.183 | 0.183 | 0.183 | 0.193 | RANDOM | 20.351 |
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] | |
0.26 | -0.96 | -1.13 | 0.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 23.742 |
r_dihedral_angle_3_deg | 12.714 |
r_dihedral_angle_4_deg | 12.265 |
r_scangle_it | 7.859 |
r_scbond_it | 5.641 |
r_dihedral_angle_1_deg | 3.536 |
r_mcangle_it | 3.003 |
r_mcbond_it | 2.218 |
r_angle_refined_deg | 1.561 |
r_angle_other_deg | 0.986 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1444 |
Nucleic Acid Atoms | |
Solvent Atoms | 156 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
SHELX | phasing |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
CCP4 | data scaling |
SHELXD | phasing |
autoSHARP | phasing |