6F9O
Crystal structure of cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B6G |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.88 | 293 | 0.2 M ammonium acetate, 30%(w/v) PEG 4000 and 0.1 M sodium acetate trihydrate pH 4.6 and with the addition of 0.6 ul of 0.1M L-proline (Additive Screen kit, Hampton Research) to the crystallization drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.332 | α = 90 |
b = 79.451 | β = 94.98 |
c = 43.489 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RAYONIX MX-225 | Sagitally bended Si111 crystal | 2012-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.978260 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.05 | 20 | 92.2 | 0.05 | 39.7 | 5.7 | 120315 | 16.716 |
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 | 1.05 | 1.09 | 56.2 | 0.307 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1B6G | 1.05 | 20 | 114202 | 6066 | 91.98 | 0.11139 | 0.11033 | 0.13151 | RANDOM | 8.671 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.671 |
r_sphericity_free | 22.761 |
r_dihedral_angle_4_deg | 16.682 |
r_dihedral_angle_3_deg | 12.244 |
r_sphericity_bonded | 7.178 |
r_dihedral_angle_1_deg | 6.086 |
r_long_range_B_refined | 2.693 |
r_long_range_B_other | 2.693 |
r_rigid_bond_restr | 2.273 |
r_angle_refined_deg | 1.634 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2465 |
Nucleic Acid Atoms | |
Solvent Atoms | 576 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |