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Structure of Cytochrome P450 CYP109Q5 from Chondromyces apiculatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M Tris-HCl pH 8.5, 28% (w/v) PEG 3350, 0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.13 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.69 α = 90 b = 55.02 β = 91.67 c = 74.8 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS 6M-F 2017-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.55 55.02 99.8 0.05 0.04 1 11.6 3.9 52220
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.8 0.53 0.45 0.82 2 4
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 5OFQ 1.55 44.71 49666 2529 98.89 0.18669 0.18494 0.1943 0.2195 0.224 RANDOM 24.768
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] -1.76 -0.36 -1.13 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.073 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 4.942 r_long_range_B_other 4.899 r_scangle_other 3.804 r_mcangle_it 2.735 r_mcangle_other 2.735 r_scbond_other 2.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.073 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 4.942 r_long_range_B_other 4.899 r_scangle_other 3.804 r_mcangle_it 2.735 r_mcangle_other 2.735 r_scbond_other 2.661 r_scbond_it 2.659 r_mcbond_it 1.98 r_mcbond_other 1.971 r_angle_refined_deg 1.589 r_angle_other_deg 1.076 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2932 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing