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VH1-18 QxxV class antibody 09-1B12 bound to A/Perth/16/2009 H3N2 hemagglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KVN HA protomer experimental model PDB 5K9Q HC variable region without CDR3 in silico model Other phyre2 model of variable light chain without CDR3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 15% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% w/v PEG10000
Crystal Properties Matthews coefficient Solvent content 4.68 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.04 α = 90 b = 158.04 β = 90 c = 417.206 γ = 120
Symmetry Space Group P 31 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 100 PIXEL DECTRIS EIGER X 16M 2022-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 4.02 50.21 99.69 0.995 7 20.5 51070 106.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.021 4.164 0.654
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entries 5KVN & 5K9Q 4.02 50.21 1.34 51049 2003 99.77 0.2307 0.2297 0.2306 0.2544 0.2541 113.41
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.5258 f_angle_d 0.7212 f_chiral_restr 0.0632 f_plane_restr 0.0058 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21861 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1120
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing