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Crystal structure of hepatitis A virus IRES domain V in complex with Fab HAVx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KZE Fab BL3-6 4KZE, 3IVK experimental model PDB 3IVK Fab BL3-6 4KZE, 3IVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.149 α = 90 b = 100.582 β = 90 c = 236.594 γ = 90
Symmetry Space Group P 21 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 80 PIXEL DECTRIS EIGER X 16M 2017-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033202 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 2.838 29.607 99.6 0.1004 0.1088 0.04158 0.999 13.89 6.8 42565 74.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.838 2.94 96.4 0.524 0.595 1.38 6.8
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 Fab BL3-6 4KZE, 3IVK 2.838 29.607 1.38 42533 1718 99.54 0.1856 0.1856 0.188 0.2522 0.2509
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 14.003 f_angle_d 1.18 f_chiral_restr 0.055 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6696 Nucleic Acid Atoms 3934 Solvent Atoms 180 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction Aimless data scaling PHENIX phasing