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Crystal structure of ClfA in complex with the Fab fragment of Tefibazumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VR3 2VR3, 1F8T experimental model PDB 1F8T 2VR3, 1F8T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 PEG 4000, isopropanol, 0.1 M Hepes
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.287 α = 90 b = 84.086 β = 98.9 c = 48.626 γ = 90
Symmetry Space Group C 1 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 120 CCD MARRESEARCH 2007-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.979 APS 23-ID-D
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 2.4 20 100 0.09 7.3 4.3 36373
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 2VR3, 1F8T 2.4 20 34560 1812 99.31 0.21042 0.20793 0.2089 0.259 0.2578 RANDOM 66.076
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] -3.78 -0.41 -0.17 3.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.702 r_dihedral_angle_4_deg 14.93 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_1_deg 6.403 r_long_range_B_refined 4.707 r_long_range_B_other 4.669 r_scangle_other 1.928 r_mcangle_it 1.774 r_mcangle_other 1.773 r_angle_refined_deg 1.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.702 r_dihedral_angle_4_deg 14.93 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_1_deg 6.403 r_long_range_B_refined 4.707 r_long_range_B_other 4.669 r_scangle_other 1.928 r_mcangle_it 1.774 r_mcangle_other 1.773 r_angle_refined_deg 1.257 r_scbond_it 1.229 r_scbond_other 1.229 r_mcbond_it 1.12 r_mcbond_other 1.12 r_angle_other_deg 0.68 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5346 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing