3DDH
The structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 278 | 0.2M MgCl2, 0.1M HEPES pH7, 25% PEG 3350, 3% D(+) Trehalose dihydrate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.119 | α = 90 |
b = 104.222 | β = 90 |
c = 121.212 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | CUSTOM-MADE | 2007-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97855 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2 | 50 | 99.2 | 0.108 | 7.2 | 8.8 | 31723 | 31723 | -3 | 26 |
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 | 2 | 2.05 | 93 | 0.443 | 3 | 5.9 | 1939 |
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 | SAD | THROUGHOUT | 2 | 33.4 | 31604 | 31604 | 1595 | 99.22 | 0.179 | 0.179 | 0.177 | 0.223 | RANDOM | 24.487 |
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] | |
1.29 | 0.21 | -1.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.277 |
r_dihedral_angle_3_deg | 13.769 |
r_dihedral_angle_4_deg | 12.374 |
r_dihedral_angle_1_deg | 5.828 |
r_scangle_it | 3.959 |
r_scbond_it | 2.687 |
r_mcangle_it | 1.603 |
r_angle_refined_deg | 1.436 |
r_mcbond_it | 1.183 |
r_angle_other_deg | 0.925 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3565 |
Nucleic Acid Atoms | |
Solvent Atoms | 342 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MLPHARE | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
SOLVE | phasing |
RESOLVE | phasing |
ARP/wARP | model building |
CCP4 | phasing |
O | model building |
Coot | model building |