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Crystal structure of cytochrome 2B4 in complex with the anti-platelet drug ticlopidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SUO PDB ENTRY 1SUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 291 20% (w/v) PEG 8000, 0.2 M MgCl2 and 0.1 M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.19 61.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.5 α = 90 b = 93.5 β = 90 c = 137.07 γ = 120
Symmetry Space Group P 32 2 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 325 mm CCD 2009-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 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 2.67 80.973 99.8 0.101 0.101 4.9 7.2 20223
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) 1 2.67 2.81 100 0.416 0.416 1.7 7.2
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 (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 PDB ENTRY 1SUO 2.67 68.54 24605 19135 1028 99.6 0.198 0.195 0.1967 0.253 0.259 RANDOM 67.3
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] -5.735 -5.735 11.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.84 r_dihedral_angle_4_deg 22.894 r_dihedral_angle_3_deg 18.074 r_dihedral_angle_1_deg 5.844 r_scangle_it 4.317 r_scbond_it 2.554 r_mcangle_it 1.736 r_angle_refined_deg 1.406 r_mcbond_it 0.897 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.84 r_dihedral_angle_4_deg 22.894 r_dihedral_angle_3_deg 18.074 r_dihedral_angle_1_deg 5.844 r_scangle_it 4.317 r_scbond_it 2.554 r_mcangle_it 1.736 r_angle_refined_deg 1.406 r_mcbond_it 0.897 r_chiral_restr 0.084 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3693 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 208
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction