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Crystal Structure of P450BM3 with N-(3-cyclopentylpropanoyl)-L-pipecolyl-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-(3-cyclopentylpropanoyl)-L-pipecolyl-L-phenylalanine, MgCl, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.63 53.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.854 α = 90 b = 148.303 β = 98.61 c = 63.691 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 EIGER R 4M 2019-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
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 1.74 48 99.1 0.118 0.126 0.045 0.999 13.2 7.7 109197
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 1.74 1.77 98.1 1.591 1.704 0.609 0.517 7.7
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 1.74 48 103701 5450 99.04 0.1734 0.1718 0.1808 0.2029 0.2087 RANDOM 22.927
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.562 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 13.809 r_dihedral_angle_1_deg 6.99 r_angle_refined_deg 1.638 r_angle_other_deg 1.418 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.562 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 13.809 r_dihedral_angle_1_deg 6.99 r_angle_refined_deg 1.638 r_angle_other_deg 1.418 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7326 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 298
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction