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crystal structure of a P450 BM3 heme domain mutant in complex with Zearalenone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.1 M TRIS 8.5; 0.2 M MgCl2; 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.843 α = 90 b = 145.286 β = 97.46 c = 61.904 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 CCD ADSC QUANTUM 315r 2019-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 1.8 25 90.8 0.037 26.4 3.3 85559
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 1.8 1.86 0.089
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 24.76 81203 4110 90.04 0.15453 0.15286 0.1652 0.1877 0.1965 RANDOM 21.16
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] -0.29 0.21 0.32 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.272 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_4_deg 13.194 r_dihedral_angle_1_deg 6.936 r_long_range_B_refined 5.911 r_long_range_B_other 5.911 r_scangle_other 4.7 r_scbond_it 3.131 r_scbond_other 3.131 r_mcangle_other 2.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.272 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_4_deg 13.194 r_dihedral_angle_1_deg 6.936 r_long_range_B_refined 5.911 r_long_range_B_other 5.911 r_scangle_other 4.7 r_scbond_it 3.131 r_scbond_other 3.131 r_mcangle_other 2.902 r_mcangle_it 2.901 r_mcbond_it 2.092 r_mcbond_other 2.09 r_angle_refined_deg 1.81 r_angle_other_deg 1.464 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7280 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement SAINT data scaling PDB_EXTRACT data extraction SAINT data reduction PHASER phasing