Crystal Structure Of Cytochrome P450 2B35 from Desert Woodrat Neotoma Lepida in complex with 4-(4-chlorophenyl)imidazole
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1SUO | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 291 | 30% (v/v) PEG400, 0.1M Hepes, 0.2 M NaCl, and 0.2 M calcium acetate, 0.1 M Tris, 15% w/v PEG4000 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.9 | 57.65 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 98.079 | α = 64.61 |
| b = 106.066 | β = 82.53 |
| c = 106.198 | γ = 69.93 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2015-01-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 0.98 | SSRL | BL7-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.4 | 40 | 94.9 | 0.238 | 6.8 | 6.7 | 141968 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 2.4 | 2.46 | 82 | 2 | |||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1SUO | 2.4 | 40 | 128121 | 6567 | 94.9 | 0.22 | 0.216 | 0.23 | 0.283 | 0.28 | RANDOM | 44.79 | ||||
| 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] | |
| -0.92 | 1.29 | -2.35 | -2 | 1.8 | 1.11 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.766 |
| r_dihedral_angle_4_deg | 20.33 |
| r_dihedral_angle_3_deg | 17.998 |
| r_dihedral_angle_1_deg | 6.721 |
| r_scangle_it | 3.726 |
| r_scbond_it | 2.322 |
| r_angle_refined_deg | 1.728 |
| r_mcangle_it | 1.511 |
| r_mcbond_it | 0.802 |
| r_chiral_restr | 0.11 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 21892 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 659 |
| Heterogen Atoms | 467 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Blu-Ice | data collection |
| SCALA | data scaling |
| PHENIX | phasing |
| MOSFLM | data reduction |
