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Crystal structure of cytochrome 2B4 in complex with the anti-platelet drug clopidogrel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 291 20% (w/v) PEG 8000, 0.2 M NaCl and 0.1 M phosphate-citrate, pH 4.2, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.2 70.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.49 α = 90 b = 234.49 β = 90 c = 57.32 γ = 120
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 325 mm CCD 2009-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.1 76.755 97.7 0.13 0.13 4.7 4 62529 62529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.1 3.18 98.6 0.432 0.432 3.5 3.9 9259
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 1SUO 3.1 76.75 62529 62516 3169 97.67 0.181 0.181 0.178 0.1784 0.234 0.2271 RANDOM 42.197
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] -0.06 -0.03 -0.06 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_4_deg 21.325 r_dihedral_angle_3_deg 19.993 r_dihedral_angle_1_deg 7.116 r_scangle_it 4.267 r_scbond_it 2.404 r_angle_refined_deg 1.936 r_mcangle_it 1.715 r_mcbond_it 0.864 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_4_deg 21.325 r_dihedral_angle_3_deg 19.993 r_dihedral_angle_1_deg 7.116 r_scangle_it 4.267 r_scbond_it 2.404 r_angle_refined_deg 1.936 r_mcangle_it 1.715 r_mcbond_it 0.864 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14882 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 256
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction