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Crystal structure of cytochrome P450 CYP121 F338H from M. tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 278 2 M ammonium sulphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.226 α = 90 b = 77.226 β = 90 c = 263.253 γ = 120
Symmetry Space Group P 65 2 2
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 210 2007-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.96 ESRF ID14-1
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 1.9 66 99.99 0.082 35865
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 FOURIER SYNTHESIS THROUGHOUT 1N40 1.9 66.82 35865 35865 1920 99.99 0.1758 0.1758 0.17352 0.1819 0.21746 0.229 RANDOM 21.174
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.322 r_dihedral_angle_4_deg 17.826 r_dihedral_angle_3_deg 13.902 r_dihedral_angle_1_deg 5.639 r_scangle_it 3.107 r_scbond_it 2.111 r_angle_other_deg 1.795 r_angle_refined_deg 1.595 r_mcangle_it 1.391 r_mcbond_it 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.322 r_dihedral_angle_4_deg 17.826 r_dihedral_angle_3_deg 13.902 r_dihedral_angle_1_deg 5.639 r_scangle_it 3.107 r_scbond_it 2.111 r_angle_other_deg 1.795 r_angle_refined_deg 1.595 r_mcangle_it 1.391 r_mcbond_it 0.953 r_mcbond_other 0.25 r_symmetry_vdw_other 0.232 r_nbd_refined 0.22 r_nbd_other 0.198 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.151 r_symmetry_vdw_refined 0.13 r_chiral_restr 0.098 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.071 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3080 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling REFMAC phasing