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Triple ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PO5 ensemble of PDB entries 1PO5, 2BDM, 1SUO, 2Q6N experimental model PDB 2BDM ensemble of PDB entries 1PO5, 2BDM, 1SUO, 2Q6N experimental model PDB 1SUO ensemble of PDB entries 1PO5, 2BDM, 1SUO, 2Q6N experimental model PDB 2Q6N ensemble of PDB entries 1PO5, 2BDM, 1SUO, 2Q6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 0.1 M HEPES, 10% 2-methyl-2,4-pentanediol, 10% PEG 6000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.78 55.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.696 α = 90 b = 152.526 β = 90 c = 181.903 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 2007-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.98 SSRL BL9-1
Data Collection Overall 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 2.5 48.457 97.2 0.083 0.083 5.641 3.5 81702 1 1 56.03
Highest Resolution Shell 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) 2.5 2.56 93.3 0.656 0.656 1.1 3.4 5714
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 ensemble of PDB entries 1PO5, 2BDM, 1SUO, 2Q6N 2.5 45.476 1.34 81584 4088 97.01 0.2199 0.2184 0.2466 0.2375 random 62.828
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] 3.7066 -1.9532 -1.7534
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.446 f_angle_d 1.838 f_chiral_restr 0.125 f_bond_d 0.02 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14102 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 452
Software Software Software Name Purpose Blu-Ice data collection PHASES phasing PHENIX refinement MOSFLM data reduction SCALA data scaling