3TIK
Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in complex with the tipifarnib derivative 6-((4-chlorophenyl)(methoxy)(1-methyl-1H-imidazol-5-yl)methyl)-4-(2,6-difluorophenyl)-1-methylquinolin-2(1H)-one
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3G1Q | PDB entry 3g1q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.4 | 297 | POTASSIUM PHOSPHATE, SODIUM CHLORIDE, GLYCEROL, PEG 5000, n-TETRADECYL-BETA-D-MALTOSIDE, 6-((4-CHLOROPHENYL)(METHOXY)(1-METHYL-1H-IMIDAZOL-YL)METHYL)-4-(2,6-DIFLUOROPHENYL)-1-METHYLQUINOLIN-2(1H)-ONE, pH 7.4, VAPOR DIFFUSION, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.722 | α = 74.47 |
b = 79.715 | β = 81.58 |
c = 117.521 | γ = 68.05 |
Symmetry | |
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Space Group | P 1 |
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 | MARMOSAIC 225 mm CCD | Be Lenses/Diamond Laue Mono | 2011-08-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.05 | 50 | 94 | 0.049 | 43.6 | 6 | 122058 | 115222 | 2.8 | 2.8 | 38.7 |
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 | 2.05 | 2.09 | 95.4 | 0.695 | 2.8 | 5.9 | 8174 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3g1q | 2.05 | 30 | 122058 | 115222 | 6082 | 99.39 | 0.18887 | 0.18887 | 0.18593 | 0.24338 | RANDOM | 49.848 |
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] | |
0.88 | -0.23 | 0.9 | -1.21 | -0.65 | 0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.132 |
r_dihedral_angle_4_deg | 19.828 |
r_dihedral_angle_3_deg | 17.457 |
r_scangle_it | 7.841 |
r_dihedral_angle_1_deg | 6.315 |
r_scbond_it | 5.147 |
r_mcangle_it | 3.311 |
r_rigid_bond_restr | 2.838 |
r_mcbond_it | 1.963 |
r_angle_refined_deg | 1.135 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14300 |
Nucleic Acid Atoms | |
Solvent Atoms | 295 |
Heterogen Atoms | 316 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |