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Molecular basis for antibody-mediated neutralization of New World hemorrhagic fever mammarenaviruses
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KAS 3KAS, 3FMG experimental model PDB 3FMG 3KAS, 3FMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 JUNV GP1 and GD01 Fab, when mixed in equimolar ratio crystallized in mother liquor containing 24% PEG 3350 (v/v), 10 mM Tris, pH 8.0, 150 mM NaCl.
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.11 α = 90 b = 74.79 β = 90 c = 177.64 γ = 90
Symmetry Space Group P 21 21 21
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 PSI PILATUS 6M 2014-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97890 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.821 68.93 99.9 0.226 0.248 0.101 6.7 5.9 63113 63113 20.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.92 99.9 1.418 1.418 0.648 0.5 5.7 9075
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 3KAS, 3FMG 1.821 68.93 63032 3168 99.69 0.1827 0.1805 0.1901 0.2244 0.2369 RANDOM 25.51
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] 2.0897 -0.42 -1.6697
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.33 t_omega_torsion 3.86 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.33 t_omega_torsion 3.86 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4459 Nucleic Acid Atoms Solvent Atoms 886 Heterogen Atoms 125
Software Software Software Name Purpose BUSTER-TNT refinement iMOSFLM data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction