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The crystal structure of Epitope III of HCV envelop protein E2 in complex with antibody 1H8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 20% PEG3350
0.1 M citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.683 α = 90 b = 42.793 β = 109.533 c = 110.824 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 CCD ADSC QUANTUM 315 2014-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.85 50 95.3 0.091 0.11 0.06 8.1 2.9 73746
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 1.85 1.88 70.2 0.511 0.66 0.412 0.476 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ZEA 2 35.699 60144 3030 98.416 0.248 0.2454 0.2467 0.2944 0.2936 27.752
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] -2.078 0.388 2.005 -0.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 18.939 r_dihedral_angle_1_deg 16.619 r_dihedral_angle_3_deg 14.485 r_lrange_it 5.094 r_lrange_other 5.076 r_angle_refined_deg 1.513 r_angle_other_deg 1.21 r_mcangle_it 0.997 r_mcangle_other 0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 18.939 r_dihedral_angle_1_deg 16.619 r_dihedral_angle_3_deg 14.485 r_lrange_it 5.094 r_lrange_other 5.076 r_angle_refined_deg 1.513 r_angle_other_deg 1.21 r_mcangle_it 0.997 r_mcangle_other 0.997 r_scangle_it 0.741 r_scangle_other 0.741 r_mcbond_it 0.538 r_mcbond_other 0.538 r_scbond_it 0.412 r_scbond_other 0.412 r_symmetry_nbd_refined 0.275 r_nbd_other 0.244 r_symmetry_xyhbond_nbd_refined 0.241 r_nbd_refined 0.195 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_other 0.116 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6557 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing