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Crystal structure of a P450 BM3 heme domain mutant
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 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.95 α = 90 b = 146.841 β = 97.56 c = 63.383 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 2019-10-08 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 1.57 25 97 0.04 35.4 4.8 145933
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 1.57 1.63 93 0.4
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 1.57 24.75 134047 7252 95.2 0.14746 0.14576 0.159 0.17881 0.187 RANDOM 16.039
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] -0.23 0.05 0.01 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.508 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 12.595 r_dihedral_angle_1_deg 6.544 r_long_range_B_refined 5.713 r_long_range_B_other 5.544 r_scangle_other 4.264 r_scbond_it 2.8 r_scbond_other 2.8 r_mcangle_it 2.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.508 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 12.595 r_dihedral_angle_1_deg 6.544 r_long_range_B_refined 5.713 r_long_range_B_other 5.544 r_scangle_other 4.264 r_scbond_it 2.8 r_scbond_other 2.8 r_mcangle_it 2.498 r_mcangle_other 2.498 r_angle_refined_deg 1.874 r_mcbond_it 1.661 r_mcbond_other 1.657 r_angle_other_deg 1.542 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7289 Nucleic Acid Atoms Solvent Atoms 1203 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement SAINT data scaling PDB_EXTRACT data extraction SAINT data reduction PHASER phasing