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Structural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N67 PDB ENTRY 1N67
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 16-20% PEG 8000, 100MM SUCCINIC ACID PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.427 α = 85.44 b = 61.836 β = 81.84 c = 81.777 γ = 82.45
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.95 15 93.9 0.07 5.8 1.9 49456
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 1.95 2.02 88.7 0.198 2.7 1.75
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 PDB ENTRY 1N67 1.95 15 45132 941 93.16 0.21264 0.21116 0.2132 0.27931 0.2839 RANDOM 29.927
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] 1.4 0.63 -0.27 0.82 -0.3 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.094 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_4_deg 12.466 r_dihedral_angle_1_deg 7.367 r_angle_refined_deg 1.642 r_nbtor_refined 0.332 r_symmetry_vdw_refined 0.322 r_xyhbond_nbd_refined 0.3 r_nbd_refined 0.259 r_symmetry_hbond_refined 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.094 r_dihedral_angle_3_deg 15.073 r_dihedral_angle_4_deg 12.466 r_dihedral_angle_1_deg 7.367 r_angle_refined_deg 1.642 r_nbtor_refined 0.332 r_symmetry_vdw_refined 0.322 r_xyhbond_nbd_refined 0.3 r_nbd_refined 0.259 r_symmetry_hbond_refined 0.181 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4699 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement