4DW8
Crystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Na crystal form I
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NIW | PDB ENTRY 3NIW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.75 | 298 | protein solution: 10 mM HEPES, pH 7.8, 150 mM sodium chloride, 10% glycerol, 5 mM magnesium, reservoir solution: 20% PEG4000, 100 mM sodium acetate, pH 4.75, 200 mM ammonium acetate, 12% ethylene glycol, cryoprotectant: reservoir solution + 10% glycerol + 10% ethylene glycol + 200 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.669 | α = 90 |
b = 73.133 | β = 90 |
c = 82.572 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | RAYONIX MX225HE | mirrors | 2011-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
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 | 1.5 | 40 | 99 | 0.056 | 0.056 | 15.9 | 6.5 | 42541 | 42541 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.5 | 1.53 | 99.4 | 0.449 | 6.2 | 2077 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | 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 | MOLECULAR REPLACEMENT | PDB ENTRY 3NIW | 1.502 | 20.281 | 40830 | 40830 | 1906 | 95.1 | 0.1824 | 0.1824 | 0.181 | 0.211 | RANDOM | 23.8647 |
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] | |
4.9275 | -2.059 | -2.8684 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.848 |
f_angle_d | 1.455 |
f_chiral_restr | 0.1 |
f_bond_d | 0.013 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2077 |
Nucleic Acid Atoms | |
Solvent Atoms | 232 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
HKL-3000 | data reduction |
PHENIX | phasing |