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Crystal structure of human CYP7A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IAG pdb entry 2iag
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 291 20% PEG400, 0.1M potassium chloride, 0.1M trisodium citrate, pH 5.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3 58.3 3 58.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.339 α = 64.36 b = 80.159 β = 75.23 c = 84.937 γ = 72.17
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2007-09-21 M SINGLE WAVELENGTH 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.96860 NSLS X25 2
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 2.1 40 92 0.063 11.1 3.7 65596
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) 2.1 2.18 68.2 0.402 3.1 4818
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 mr, MR THROUGHOUT pdb entry 2iag 2.15 30 63038 2018 93.449 0.19 0.189 0.1922 0.228 0.2289 thin shells (sftools) 31.625
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] -0.061 -0.162 -0.007 0.081 0.19 -0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.131 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_3_deg 14.595 r_dihedral_angle_1_deg 5.969 r_mcangle_it 3.606 r_scangle_it 3.393 r_mcbond_it 2.526 r_scbond_it 2.432 r_angle_refined_deg 1.288 r_angle_other_deg 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.131 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_3_deg 14.595 r_dihedral_angle_1_deg 5.969 r_mcangle_it 3.606 r_scangle_it 3.393 r_mcbond_it 2.526 r_scbond_it 2.432 r_angle_refined_deg 1.288 r_angle_other_deg 0.877 r_mcbond_other 0.615 r_symmetry_hbond_refined 0.217 r_symmetry_vdw_other 0.205 r_nbd_refined 0.202 r_nbd_other 0.188 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.122 r_symmetry_vdw_refined 0.098 r_nbtor_other 0.086 r_chiral_restr 0.079 r_bond_refined_d 0.017 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7519 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 88
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling Coot model building MolProbity model building