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Crystal Structure of P450BM3 with N-enanthoyl-L-prolyl-L-phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.9 293 Tris-HCl, 0.1% (v/v) dimethyl sulfoxide, 0.1mM N-heptanoyl-L-prolyl-L-phenylalanine, MgCl, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.7 54.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.828 α = 90 b = 128.427 β = 90 c = 148.889 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 EIGER2 X 9M 2018-10-10 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) 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 1.84 48.62 100 0.147 0.152 0.041 0.999 13.4 13.7 98678
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 1.84 1.87 100 2.416 2.505 0.66 0.543 14.3
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 5XA3 1.84 48.62 93664 4925 99.99 0.1931 0.1913 0.1989 0.2258 0.2331 RANDOM 29.277
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.064 r_dihedral_angle_4_deg 17.47 r_dihedral_angle_3_deg 15.273 r_dihedral_angle_1_deg 7.03 r_angle_refined_deg 1.638 r_angle_other_deg 1.358 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.064 r_dihedral_angle_4_deg 17.47 r_dihedral_angle_3_deg 15.273 r_dihedral_angle_1_deg 7.03 r_angle_refined_deg 1.638 r_angle_other_deg 1.358 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7328 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction