5HDI
Structural characterization of CYP144A1, a Mycobacterium tuberculosis cytochrome P450
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2XKR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | Crystallography was performed using the sitting drop method using 20 mg/ml CYP144A1. Drops were prepared by the addition of 0.2 microl of CYP144A1-FLV and -TRV proteins to 0.2 microl of mother liquor and by incubating at 4 oC. Following initial crystallogenesis using commercial screens, crystallization conditions were further refined to 0.8 or 1.0 M (NH4)2SO4 with 0.1 M HEPES, pH 7.55, and 25% PEG 3350. Single crystals were flash cooled after addition of 10% PEG 200 as cryoprotectant |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.35 | α = 90 |
b = 117.79 | β = 90 |
c = 122.09 | 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 | PIXEL | PSI PILATUS 6M | 2014-08-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.00 | Diamond | I03 |
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 | 1.54 | 88.58 | 98.7 | 0.097 | 10.4 | 4.4 | 116903 | 15.8 |
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 | 1.54 | 1.58 | 97.1 | 0.807 | 2.3 | 4.4 |
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 | 2XKR | 1.54 | 84.77 | 116903 | 6118 | 98.45 | 0.14028 | 0.13761 | 0.19238 | RANDOM | 22.554 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
2.01 | -2.08 | 0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.219 |
r_sphericity_free | 26.91 |
r_dihedral_angle_4_deg | 18.53 |
r_sphericity_bonded | 17.578 |
r_dihedral_angle_3_deg | 12.953 |
r_rigid_bond_restr | 7.629 |
r_dihedral_angle_1_deg | 5.672 |
r_angle_refined_deg | 1.872 |
r_angle_other_deg | 0.987 |
r_chiral_restr | 0.126 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6044 |
Nucleic Acid Atoms | |
Solvent Atoms | 546 |
Heterogen Atoms | 86 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |