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Crystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 293 75mM Tris-HCl (pH7.9), 50uM N-perfluorononanoyl L-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 105mM MgCl and 10.5% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.875 α = 90 b = 145.392 β = 97.06 c = 63.029 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 MAR225 2013-12-16 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 1.8 20 94.9 0.059 11.7 3.2 91778 -3 16.083
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 1.8 1.86 98.5 0.3 3.1 9454
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZO9 1.8 19.96 91739 4600 94.26 0.176 0.1741 0.2122 0.2226 RANDOM 22.965
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 34.674 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 14.312 r_dihedral_angle_1_deg 6.813 r_angle_refined_deg 1.099 r_angle_other_deg 0.682 r_chiral_restr 0.165 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.674 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 14.312 r_dihedral_angle_1_deg 6.813 r_angle_refined_deg 1.099 r_angle_other_deg 0.682 r_chiral_restr 0.165 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7310 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 178
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction