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Human cytochrome P450 2E1 in complex with omega-imidazolyl-decanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E61 PDB entry 3E61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M Na HEPES, 5% Isopropanol, 20% PEG 2000 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.709 α = 90 b = 70.709 β = 90 c = 222.823 γ = 90
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 MAR CCD 165 mm Sagitally focused second crystal, vertical focusing via a one-meter, Pt/Pd-coated cylindrically focusing mirror 2008-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM 1.000 APS 17-BM
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 2.7 50 95.4 0.104 17.071 6.7 28495 28493 51.075
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) 2.7 2.8 93.4 0.457 6.3 2034
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 PDB entry 3E61 2.7 31.31 27040 1442 95.49 0.21609 0.21245 0.2101 0.28261 0.2801 RANDOM 28.748
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.537 r_dihedral_angle_4_deg 24.048 r_dihedral_angle_3_deg 21.783 r_dihedral_angle_1_deg 7.517 r_scangle_it 2.797 r_angle_refined_deg 1.909 r_scbond_it 1.828 r_mcangle_it 1.172 r_mcbond_it 0.677 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.537 r_dihedral_angle_4_deg 24.048 r_dihedral_angle_3_deg 21.783 r_dihedral_angle_1_deg 7.517 r_scangle_it 2.797 r_angle_refined_deg 1.909 r_scbond_it 1.828 r_mcangle_it 1.172 r_mcbond_it 0.677 r_nbtor_refined 0.315 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7530 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 120
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling