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Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-prolyl-L-phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 293 75mM Tris-HCl (pH7.9), 0.1% (v/v) dimethyl sulfoxide, 0.1mM Benzyloxycarbonyl-L-prolyl-L-phenylalanine, 60mM MgCl, 10.5% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.58 52.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.234 α = 90 b = 58.522 β = 90.02 c = 145.952 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 CCD MARMOSAIC 225 mm CCD 2015-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 145.95 97.1 0.09 6.9 2.4 105865
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 95.3 0.366 2.3
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 3WSP 2.2 50 100612 5243 97 0.222 0.221 0.2247 0.253 0.2554 RANDOM 20.39
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] -0.02 -0.02 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.668 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_4_deg 11.772 r_dihedral_angle_1_deg 5.751 r_angle_refined_deg 1.159 r_angle_other_deg 0.932 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.668 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_4_deg 11.772 r_dihedral_angle_1_deg 5.751 r_angle_refined_deg 1.159 r_angle_other_deg 0.932 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14620 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 304
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction DENZO data reduction