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Atomic structure of the heme domain of flavocytochrome P450-BM3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 PEG and Magnesium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.448 α = 90 b = 153.426 β = 94.72 c = 59.69 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 ADSC QUANTUM 210 2004-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.2 20 99.2 0.071 11.1 312598 312598
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1BU7 1.2 19.83 312598 312598 16593 99.2 0.1487 0.1487 0.14779 0.1577 0.16561 0.1761 RANDOM 16.713
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] 0.1 0.04 -0.14 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.217 r_dihedral_angle_4_deg 15.155 r_dihedral_angle_3_deg 12.254 r_sphericity_free 6.422 r_dihedral_angle_1_deg 6.025 r_sphericity_bonded 3.938 r_scangle_it 3.766 r_scbond_it 2.887 r_rigid_bond_restr 2.35 r_mcangle_it 2.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.217 r_dihedral_angle_4_deg 15.155 r_dihedral_angle_3_deg 12.254 r_sphericity_free 6.422 r_dihedral_angle_1_deg 6.025 r_sphericity_bonded 3.938 r_scangle_it 3.766 r_scbond_it 2.887 r_rigid_bond_restr 2.35 r_mcangle_it 2.056 r_mcbond_it 1.633 r_angle_refined_deg 1.517 r_angle_other_deg 0.884 r_mcbond_other 0.737 r_symmetry_vdw_other 0.297 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.226 r_nbd_other 0.184 r_nbtor_refined 0.184 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.1 r_xyhbond_nbd_other 0.094 r_nbtor_other 0.084 r_bond_refined_d 0.013 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 7337 Nucleic Acid Atoms Solvent Atoms 1606 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing