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Crystal structure of Fab fragment of Anti-HCV E2 antibody (HC84.26)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ESA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 0.4 M Ammonium Acetate,
20% PEG 2000 MME,
Cryoprotectant-Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.88 57.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.535 α = 90 b = 113.699 β = 90 c = 122.696 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 100 PIXEL DECTRIS EIGER X 16M 2019-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.979 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 50 99.8 0.053 0.059 0.025 0.996 26.41 5.1 53599 28.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 99.9 0.649 0.728 0.326 0.771 2.18 4.8
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 5ESA 1.8 34.9 50913 2648 99.68 0.17993 0.17839 0.19 0.20966 0.2176 RANDOM 41.292
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] -0.35 -0.31 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.461 r_dihedral_angle_4_deg 21.404 r_dihedral_angle_1_deg 18.673 r_dihedral_angle_3_deg 12.097 r_long_range_B_refined 7.926 r_long_range_B_other 7.864 r_scangle_other 5.061 r_mcangle_it 3.795 r_mcangle_other 3.795 r_scbond_other 3.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.461 r_dihedral_angle_4_deg 21.404 r_dihedral_angle_1_deg 18.673 r_dihedral_angle_3_deg 12.097 r_long_range_B_refined 7.926 r_long_range_B_other 7.864 r_scangle_other 5.061 r_mcangle_it 3.795 r_mcangle_other 3.795 r_scbond_other 3.337 r_scbond_it 3.336 r_mcbond_it 2.429 r_mcbond_other 2.428 r_angle_refined_deg 1.472 r_angle_other_deg 1.072 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling PHASER phasing