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Crystal Structure of Cytochrome P450BM3 III-10C1 Mutant Heme Domain with N-Decanoyl-L-Homoserine Lactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JLV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.4 293 PEG 8000, Tris-HCl, magnesium chloride, N-decanoyl homoserine lactone
Crystal Properties Matthews coefficient Solvent content 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.575 α = 90 b = 145.442 β = 97.37 c = 63.106 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 PILATUS3 X 6M 2021-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
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 1.46 47.44 98.1 0.101 0.11 0.045 0.993 11.6 5.9 177212
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 1.46 1.48 97.1 0.745 0.838 0.376 0.686 2.1 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.46 47.44 168167 9001 98 0.16661 0.16575 0.18242 0.1938 RANDOM 18.88
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] -0.56 -0.11 -0.17 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.619 r_dihedral_angle_4_deg 17.101 r_dihedral_angle_3_deg 13.204 r_dihedral_angle_1_deg 6.554 r_long_range_B_refined 5.214 r_long_range_B_other 5.152 r_scangle_other 4.284 r_scbond_it 2.853 r_scbond_other 2.852 r_mcangle_it 2.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.619 r_dihedral_angle_4_deg 17.101 r_dihedral_angle_3_deg 13.204 r_dihedral_angle_1_deg 6.554 r_long_range_B_refined 5.214 r_long_range_B_other 5.152 r_scangle_other 4.284 r_scbond_it 2.853 r_scbond_other 2.852 r_mcangle_it 2.599 r_mcangle_other 2.599 r_angle_refined_deg 1.825 r_mcbond_it 1.821 r_mcbond_other 1.817 r_angle_other_deg 1.548 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 7338 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction