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CYP153A71 from Acinetobacter dieselolei bound to octanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 289 0.1 M HEPES pH 7.5
12% (w/v) polyethylene glycol 3350
10 mM octanoic acid
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.661 α = 90 b = 76.817 β = 90.53 c = 107.344 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 100 PIXEL DECTRIS PILATUS3 6M 2018-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.95 46.11 97.8 0.129 0.154 0.083 0.995 7.2 3.4 66934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 97 1.365 1.615 0.857 0.519 3.5
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 5FYF 1.95 46.11 63554 3379 97.81 0.2311 0.229 0.2338 0.2707 0.2738 RANDOM 40.926
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] 5.17 3.75 -2.65 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.019 r_dihedral_angle_3_deg 14.847 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_1_deg 6.333 r_angle_refined_deg 1.256 r_angle_other_deg 1.12 r_chiral_restr 0.051 r_bond_other_d 0.005 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.019 r_dihedral_angle_3_deg 14.847 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_1_deg 6.333 r_angle_refined_deg 1.256 r_angle_other_deg 1.12 r_chiral_restr 0.051 r_bond_other_d 0.005 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6843 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction autoPROC data reduction