4WDQ
Crystal structure of haloalkane dehalogenase LinB32 mutant (L177W) from Sphingobium japonicum UT26
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 295 | 0.1M MES; 0.2M MgCl2; 25% PEG3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.94 | 36.72 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 46.729 | α = 90 |
b = 68.49 | β = 90 |
c = 81.055 | γ = 90 |
Symmetry | |
---|---|
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 | MAR CCD 165 mm | 2011-12-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8123 | EMBL/DESY, HAMBURG | X13 |
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 | 1.57 | 50 | 98.3 | 0.094 | 6.5 | 6.9 | 37131 | 36500 |
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 | 1.57 | 1.63 | 85.2 | 0.285 | 5.4 | 3111 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1CV2 | 1.58 | 40.49 | 36137 | 1802 | 98.55 | 0.1619 | 0.1596 | 0.2057 | RANDOM | 12.777 |
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] | |
0.01 | -0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.3 |
r_dihedral_angle_4_deg | 18.692 |
r_dihedral_angle_3_deg | 11.899 |
r_dihedral_angle_1_deg | 5.993 |
r_scangle_it | 2.686 |
r_scbond_it | 1.762 |
r_angle_refined_deg | 1.399 |
r_mcangle_it | 1.005 |
r_mcbond_it | 0.716 |
r_nbtor_refined | 0.314 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2353 |
Nucleic Acid Atoms | |
Solvent Atoms | 714 |
Heterogen Atoms | 5 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-3000 | data reduction |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Coot | model building |
HKL-3000 | data scaling |