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Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Diffraction quality crystals grew in about a week in hanging drops where 3 ul of the MEDI4893 Fab/AT complex at a concentration of 15 mg/ml in 50 mM Tris-HCl, pH 7.5, 100 mM NaCl was mixed with 2 ul of 10% (w/v) PEG 6000, 100 mM HEPES, pH 7.0 and let to equilibrate against 300 ul of 10% (w/v) PEG 6000, 100 mM HEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.5 64.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.524 α = 90 b = 148.505 β = 99.82 c = 93.824 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 PIXEL DECTRIS PILATUS 6M 2011-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
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 2.56 92.45 97.5 0.103 11.5 5.3 74008 53
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 2.56 2.75 98.6 1.54 1.3 5.9
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 7AHL 2.56 92.45 69982 3716 99.35 0.19966 0.1978 0.2053 0.23488 0.2366 RANDOM 43.455
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] -0.6 -0.57 2.5 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_4_deg 18.239 r_dihedral_angle_3_deg 16.478 r_dihedral_angle_1_deg 7.068 r_long_range_B_refined 6.061 r_long_range_B_other 6.048 r_scangle_other 3.893 r_mcangle_it 3.221 r_mcangle_other 3.221 r_scbond_it 2.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_4_deg 18.239 r_dihedral_angle_3_deg 16.478 r_dihedral_angle_1_deg 7.068 r_long_range_B_refined 6.061 r_long_range_B_other 6.048 r_scangle_other 3.893 r_mcangle_it 3.221 r_mcangle_other 3.221 r_scbond_it 2.586 r_scbond_other 2.432 r_mcbond_it 2.022 r_mcbond_other 2.022 r_angle_refined_deg 1.371 r_angle_other_deg 0.848 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 10934 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement