4I3Q
Crystal structure of human CYP3A4 coordinated to a water molecule
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WOE | PDB ENTRY 1WOE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | microbatch under oil | 6 | 298 | PEG 3350, sodium malonate, pH 6.0, microbatch under oil, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.11 | α = 90 |
b = 101.47 | β = 90 |
c = 130.54 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | 200 | CCD | ADSC QUANTUM 315 | mirrors | 2012-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.127 | SSRL | BL7-1 |
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 | 2.6 | 65.3 | 98.4 | 0.082 | 10.3 | 7.1 | 16524 | 16260 | 2 |
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 | 2.6 | 2.67 | 97.5 | 0.516 | 2.3 | 4.5 |
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 | PHASER | THROUGHOUT | PDB ENTRY 1WOE | 2.602 | 65.27 | 15432 | 819 | 98.39 | 0.22355 | 0.21999 | 0.29814 | RANDOM | 93.672 |
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] | |
0.09 | -0.05 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.998 |
r_dihedral_angle_3_deg | 19.75 |
r_dihedral_angle_4_deg | 18.884 |
r_dihedral_angle_1_deg | 6.541 |
r_angle_refined_deg | 1.998 |
r_chiral_restr | 0.101 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3749 |
Nucleic Acid Atoms | |
Solvent Atoms | 6 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |