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Crystal structure of Hepatitis C Virus E1 glycoprotein epitope 314-324 scaffold design 1W4K_08 in complex with neutralizing antibody F(ab) fragment IGH526
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M Ammonium acetate 0.1 M BIS-Tris 5.5 25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.32 α = 90 b = 121.76 β = 90 c = 234.1 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 DECTRIS EIGER X 9M 2019-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.0007 SOLEIL PROXIMA 2
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 2.59 48.63 99.41 0.997 11.18 13.6 64890 70.17
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 2.593 2.686 97.58 0.564 0.74 13.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.59 48.63 1.34 64595 3227 99.43 0.234 0.2319 0.2372 0.2731 0.2745 77.91
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 12.5016 f_angle_d 0.5834 f_chiral_restr 0.0433 f_plane_restr 0.0053 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13205 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling PHENIX phasing