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Structure of the Carbonylruthenium Mesoporphyrin IX-Reconstituted 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 PEG 8000, Magnesium Chloride, Tris-HCl. 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan
Crystal Properties Matthews coefficient Solvent content 2.75 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.116 α = 90 b = 128.556 β = 90 c = 149.452 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 100 PIXEL DECTRIS EIGER X 9M 2019-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00000 SPring-8 BL32XU
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 1.55 48.73 100 0.094 0.099 0.03 0.999 11 10.6 165527
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 1.55 1.58 99.5 1.528 1.653 0.617 0.551 1.1 6.7
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 1.55 46.49 157129 8259 99.91 0.169 0.1672 0.178 0.2046 0.2125 RANDOM 29.858
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.683 r_dihedral_angle_4_deg 14.852 r_dihedral_angle_3_deg 14.263 r_dihedral_angle_1_deg 6.495 r_rigid_bond_restr 2.223 r_angle_refined_deg 1.82 r_angle_other_deg 1.391 r_chiral_restr 0.153 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.683 r_dihedral_angle_4_deg 14.852 r_dihedral_angle_3_deg 14.263 r_dihedral_angle_1_deg 6.495 r_rigid_bond_restr 2.223 r_angle_refined_deg 1.82 r_angle_other_deg 1.391 r_chiral_restr 0.153 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7278 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 252
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction