☰ Navigation Tabs
Crystal Structure of Cytochrome P450BM3 V-19A14 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 2.7 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.9 α = 90 b = 148.32 β = 100.11 c = 65.33 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 2022-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.32 49.44 100 0.133 0.136 0.999 13.58 28.4 257607
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.35 100 6.932 7.058 0.579 1.45 28.2
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 1.32 48.59 244780 12849 100 0.1637 0.16286 0.1635 0.17981 0.1805 RANDOM 19.789
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] -0.7 -0.24 0.05 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.123 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_3_deg 12.217 r_dihedral_angle_1_deg 6.301 r_long_range_B_refined 5.211 r_long_range_B_other 5.138 r_scangle_other 4.606 r_scbond_it 3.11 r_scbond_other 3.11 r_mcangle_other 2.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.123 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_3_deg 12.217 r_dihedral_angle_1_deg 6.301 r_long_range_B_refined 5.211 r_long_range_B_other 5.138 r_scangle_other 4.606 r_scbond_it 3.11 r_scbond_other 3.11 r_mcangle_other 2.357 r_mcangle_it 2.355 r_angle_refined_deg 2 r_mcbond_it 1.695 r_mcbond_other 1.691 r_angle_other_deg 1.541 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 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 7328 Nucleic Acid Atoms Solvent Atoms 769 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction