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Cytochrome P450 2B4 covalently bound to the mechanism-based inactivator 9-ethynylphenanthrene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SUO PDB ENTRY 1SUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1 M Tris, 20% (w/v) PEG 3000, 0.2 M calcium acetate, pH 7.0, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.21 61.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.155 α = 90 b = 90.155 β = 90 c = 148.623 γ = 120
Symmetry Space Group P 31 2 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 APEX II CCD 2011-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.54
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 2.939 78.08 99.8 0.128 0.128 12.73 7.4 15475 15444
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 2.939 2.96 92.6 0.395 2.14 3.61 174
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SUO 2.939 78.08 15435 15379 765 99.64 0.2455 0.2455 0.2429 0.2365 0.2961 0.2849 RANDOM 28.641
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] -0.9 -0.45 -0.9 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.467 r_dihedral_angle_4_deg 14.664 r_dihedral_angle_3_deg 14.55 r_dihedral_angle_1_deg 4.774 r_angle_refined_deg 0.952 r_scangle_it 0.893 r_mcangle_it 0.501 r_scbond_it 0.486 r_mcbond_it 0.269 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.467 r_dihedral_angle_4_deg 14.664 r_dihedral_angle_3_deg 14.55 r_dihedral_angle_1_deg 4.774 r_angle_refined_deg 0.952 r_scangle_it 0.893 r_mcangle_it 0.501 r_scbond_it 0.486 r_mcbond_it 0.269 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3696 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 116
Software Software Software Name Purpose SAINT data scaling XPREP data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction