5UDA
Crystal structure of CYP2B6 (Y226H/K262R) in complex with a monoterpene bornane
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4I91 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 291 | 0.2 M Sodium Chloride 0.1 M HEPES 25% w/v Polyethylene glycol 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.24 | 62.02 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 77.49 | ¦Á = 90 |
b = 77.49 | ¦Â = 90 |
c = 202.15 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 |
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 | Marm | 2016-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97946 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.93 | 40.43 | 96.2 | 0.049 | 9.7 | 3.1 | 98894 |
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 | 1.93 | 2.03 | 97.7 | 0.229 | 3.2 | 3.1 | 14692 |
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 | 4I91 | 1.93 | 40.43 | 94042 | 4852 | 96.19 | 0.17522 | 0.17337 | 0.20993 | RANDOM | 26.458 |
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] | |
0.64 | 0.32 | 0.64 | -0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.032 |
r_dihedral_angle_4_deg | 20.16 |
r_dihedral_angle_3_deg | 14.659 |
r_dihedral_angle_1_deg | 6.071 |
r_scangle_it | 5.703 |
r_scbond_it | 3.719 |
r_mcangle_it | 2.455 |
r_angle_refined_deg | 2.199 |
r_mcbond_it | 1.424 |
r_chiral_restr | 0.17 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7416 |
Nucleic Acid Atoms | |
Solvent Atoms | 481 |
Heterogen Atoms | 222 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
PHASER | phasing |
iMOSFLM | data reduction |
SCALA | data scaling |