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Crystal Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 (P450BM3) Heme Domain with N-Dodecanoyl-L-Homoserine Lactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 277 8.5%(w/v)PEG8000, 60 mM Magnesium Chloride, 75 mM Tris-HCl, 250 uM N-Dodecanoyl-L-Homoserine Lactone, 1%(v/v) Methanol
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.295 α = 90 b = 121.827 β = 90 c = 148.689 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2021-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000000 SPring-8 BL45XU
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 1.75 49.63 99.1 0.143 0.154 0.998 9.29 7.109 107242 30.641
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 1.75 1.85 97 1.41 1.527 0.581 1.47 6.727
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6K58 1.75 49.63 101500 5329 99.36 0.1797 0.1781 0.1877 0.2099 0.2152 RANDOM 27.511
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] -1.15 2.13 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 6.482 r_angle_refined_deg 1.403 r_angle_other_deg 1.336 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 6.482 r_angle_refined_deg 1.403 r_angle_other_deg 1.336 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7335 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 146
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction