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Structure of the Chromium Protoporphyrin 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 PEG8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan
Crystal Properties Matthews coefficient Solvent content 2.44 49.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.032 α = 90 b = 148.362 β = 98.04 c = 63.524 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 4M 2018-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000000 SPring-8 BL26B1
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 1.85 48.02 98.9 0.104 10.6 6.8 90862
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 1.85 1.88 98.7 1.824 1.2 7.1
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 1.85 48.02 86335 4464 98.7 0.185 0.183 0.1833 0.221 0.2208 RANDOM 33.52
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] 0.02 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.357 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_4_deg 13.87 r_long_range_B_refined 6.663 r_dihedral_angle_1_deg 6.48 r_mcangle_it 3.638 r_scbond_it 3.567 r_mcbond_it 2.616 r_angle_refined_deg 1.521 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.357 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_4_deg 13.87 r_long_range_B_refined 6.663 r_dihedral_angle_1_deg 6.48 r_mcangle_it 3.638 r_scbond_it 3.567 r_mcbond_it 2.616 r_angle_refined_deg 1.521 r_chiral_restr 0.117 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 7348 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction MOLREP phasing