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Crystal Structure of Cytochrome P450BM3 VI-18A12 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 2.6 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.482 α = 90 b = 148.785 β = 98.91 c = 61.374 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 2022-01-19 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 2.27 47 97.6 0.319 0.351 0.141 0.97 5.5 6.1 46574
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 2.27 2.34 98 1.327 1.453 0.582 0.539 6.2
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 2.27 47 44238 2326 97.46 0.19227 0.18883 0.1954 0.25946 0.2592 RANDOM 24.172
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] -2.01 -0.79 -0.45 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.825 r_dihedral_angle_4_deg 21.13 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 6.993 r_long_range_B_refined 4.826 r_long_range_B_other 4.804 r_scangle_other 3.62 r_mcangle_it 2.811 r_mcangle_other 2.811 r_scbond_it 2.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.825 r_dihedral_angle_4_deg 21.13 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 6.993 r_long_range_B_refined 4.826 r_long_range_B_other 4.804 r_scangle_other 3.62 r_mcangle_it 2.811 r_mcangle_other 2.811 r_scbond_it 2.257 r_scbond_other 2.256 r_mcbond_it 1.816 r_mcbond_other 1.814 r_angle_refined_deg 1.698 r_angle_other_deg 1.275 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 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 7352 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction