2HI4
Crystal Structure of Human Microsomal P450 1A2 in complex with alpha-naphthoflavone
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Z10 | CYP2A6, PDB entry 1Z10 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | PEG3350, Tris, ammonium nitrate, Cymal-6 (cyclohexyl-hexyl-beta-D-maltoside), C12E8 (octaethyleneglycol mono-n-dodecyl ether) , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.63 | α = 90 |
b = 80.82 | β = 90 |
c = 175.82 | 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 | 100 | CCD | ADSC QUANTUM 315 | Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) | 2006-04-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97945 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.9 | 88.045 | 92.2 | 0.092 | 0.092 | 4 | 5 | 41139 | 41139 | 23.73 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.9 | 1.95 | 95.2 | 0.394 | 0.394 | 1.5 | 4.9 | 3092 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | CYP2A6, PDB entry 1Z10 | 1.95 | 29.51 | 39893 | 38022 | 1871 | 91.1 | 0.223 | 0.226 | 0.267 | RANDOM | 37.6 |
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] | |
24.99 | -12.86 | -12.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.3 |
c_angle_deg | 2 |
c_improper_angle_d | 1.26 |
c_bond_d | 0.019 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3844 |
Nucleic Acid Atoms | |
Solvent Atoms | 160 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
PHASER | phasing |