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Structure of CYP153A from Marinobacter aquaeolei in complex with hydroxydodecanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RWL PDB ENTRY 3RWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M BIS-TRIS PROPANE PH 5.5; 25% PEG 3350 (W/V); 30 MG PER ML PROTEIN; SOAK WITH 10 MM HYDROXYDODECANOIC ACID
Crystal Properties Matthews coefficient Solvent content 2.07 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.02 α = 90 b = 71.31 β = 90 c = 213.82 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 2015-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.22 56.89 100 0.14 10 6.6 47442 2
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) 1 2.22 2.29 100 0.63 2.6 6.8
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 3RWL 2.22 56.89 43348 2239 99.97 0.18977 0.1873 0.1953 0.23937 0.245 RANDOM 36.211
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] -1.03 1.55 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.972 r_dihedral_angle_4_deg 16.018 r_dihedral_angle_3_deg 14.96 r_dihedral_angle_1_deg 6.085 r_mcangle_it 4.016 r_scbond_it 3.296 r_mcbond_it 2.806 r_mcbond_other 2.804 r_angle_refined_deg 1.8 r_angle_other_deg 1.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.972 r_dihedral_angle_4_deg 16.018 r_dihedral_angle_3_deg 14.96 r_dihedral_angle_1_deg 6.085 r_mcangle_it 4.016 r_scbond_it 3.296 r_mcbond_it 2.806 r_mcbond_other 2.804 r_angle_refined_deg 1.8 r_angle_other_deg 1.576 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6612 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing