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Crystal structure of Fab fragment of anti-HCV E2 antibody (CBH-7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1M Sodium phosphate dibasic pH 4.2, 0.2 M NaCl, and 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.935 α = 90 b = 101.912 β = 100.24 c = 109.936 γ = 90
Symmetry Space Group C 1 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 2021-10-07 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 1.62 50 98.4 0.09 0.098 0.038 0.981 27.75 6.4 107383 19.42
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 1.62 1.65 98.5 0.544 0.595 0.238 0.911 5.6
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 6X9X 1.62 46.14 102019 5362 98.13 0.17881 0.17695 0.1784 0.21384 0.2143 RANDOM 23.222
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] 2.84 -0.37 -1.2 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.106 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 7.315 r_long_range_B_refined 6.071 r_long_range_B_other 6.071 r_scangle_other 4.463 r_scbond_other 3.021 r_scbond_it 3.02 r_mcangle_other 2.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.106 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 7.315 r_long_range_B_refined 6.071 r_long_range_B_other 6.071 r_scangle_other 4.463 r_scbond_other 3.021 r_scbond_it 3.02 r_mcangle_other 2.933 r_mcangle_it 2.932 r_mcbond_it 2.077 r_mcbond_other 2.075 r_angle_refined_deg 1.649 r_angle_other_deg 1.44 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6449 Nucleic Acid Atoms Solvent Atoms 782 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALA data scaling PHASER phasing