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Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 PEG8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.964 α = 90 b = 148.732 β = 98.38 c = 63.91 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 EIGER X 16M 2018-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8000 SPring-8 BL41XU
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 1.22 48.22 99.9 0.059 13.1 6.9 321634
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 1.22 1.24 100 1.844 1 6.9
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 3WSP 1.22 48.22 305594 15969 99.9 0.135 0.134 0.1348 0.156 0.1571 RANDOM 19.49
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] -0.53 -0.26 -0.2 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.716 r_dihedral_angle_4_deg 15.965 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_1_deg 6.543 r_angle_refined_deg 1.513 r_angle_other_deg 1.464 r_rigid_bond_restr 1.374 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.716 r_dihedral_angle_4_deg 15.965 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_1_deg 6.543 r_angle_refined_deg 1.513 r_angle_other_deg 1.464 r_rigid_bond_restr 1.374 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7342 Nucleic Acid Atoms Solvent Atoms 951 Heterogen Atoms 295
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing