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Crystal structure of CYP46A1 with [(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl][(4R,8M)-8-(1,3-oxazol-5-yl)-6-(trifluoromethyl)imidazo[1,2-a]pyridin-3-yl]methanone (compound 3k)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LRL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 18.5% PEG3350, 0.4 M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.478 α = 90 b = 63.633 β = 90 c = 124.615 γ = 90
Symmetry Space Group P 21 21 21
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 2012-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3
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 1.67 50 99.6 0.102 9.5 6.8 54937
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 1.67 1.7 94.6 0.751 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.67 30 52157 2708 99.38 0.17214 0.17027 0.20739 0.2345 RANDOM 9.055
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] 0.83 -0.87 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.906 r_sphericity_free 16.713 r_dihedral_angle_4_deg 16.632 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 5 r_sphericity_bonded 4.31 r_rigid_bond_restr 3.81 r_angle_refined_deg 2.061 r_angle_other_deg 0.946 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.906 r_sphericity_free 16.713 r_dihedral_angle_4_deg 16.632 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 5 r_sphericity_bonded 4.31 r_rigid_bond_restr 3.81 r_angle_refined_deg 2.061 r_angle_other_deg 0.946 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3499 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing