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Crystal structure of anti-Nipah virus (NiV) F 5B3 antibody Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M Magnesium chloride, 0.1 M Tris HCl, pH 8.5 and 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.7 54.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.12 α = 90 b = 95.01 β = 90 c = 137.2 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2018-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 1.48 68.6 99.7 0.08 0.088 0.036 10.2 5.6 84268
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.483 1.56 97.8 0.904 0.904 1.052 0.523 0.9 3.6
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 6NB8 1.483 68.6 79965 4238 99.61 0.139 0.1372 0.1386 0.1733 0.1724 RANDOM 21.717
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] -3.94 3.27 0.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.884 r_dihedral_angle_2_deg 30.144 r_sphericity_bonded 23.32 r_dihedral_angle_4_deg 21.125 r_dihedral_angle_1_deg 14.48 r_dihedral_angle_3_deg 11.449 r_rigid_bond_restr 3.225 r_angle_refined_deg 1.22 r_angle_other_deg 0.91 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.884 r_dihedral_angle_2_deg 30.144 r_sphericity_bonded 23.32 r_dihedral_angle_4_deg 21.125 r_dihedral_angle_1_deg 14.48 r_dihedral_angle_3_deg 11.449 r_rigid_bond_restr 3.225 r_angle_refined_deg 1.22 r_angle_other_deg 0.91 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3296 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction