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Crystal structure of human coxsackievirus A24v in complex with a pentavalent N-acetylneuraminic acid conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q4W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 200 mM Magnesium chloride, 3.4 M 1,6-Hexanediol, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 305.52 α = 90 b = 365.55 β = 90 c = 366.48 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS 6M-F 2018-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976250 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.78 49.962 99.9 0.263 0.282 0.989 6.6 7.7 1921680 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.89 99.7 1.331 1.428 0.506 1.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4Q4W 1.78 49.96 1921680 99.919 0.158 0.1577 0.4013 32.077
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] -0.059 0.19 -0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.664 r_dihedral_angle_4_deg 16.065 r_dihedral_angle_3_deg 11.772 r_dihedral_angle_1_deg 9.06 r_lrange_it 7.183 r_lrange_other 6.88 r_scangle_other 5.812 r_scangle_it 5.809 r_scbond_it 4.127 r_scbond_other 4.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.664 r_dihedral_angle_4_deg 16.065 r_dihedral_angle_3_deg 11.772 r_dihedral_angle_1_deg 9.06 r_lrange_it 7.183 r_lrange_other 6.88 r_scangle_other 5.812 r_scangle_it 5.809 r_scbond_it 4.127 r_scbond_other 4.115 r_mcangle_other 3.001 r_mcangle_it 2.998 r_mcbond_it 2.252 r_mcbond_other 2.24 r_angle_refined_deg 1.371 r_angle_other_deg 1.296 r_symmetry_nbd_refined 0.562 r_nbd_other 0.54 r_nbd_refined 0.184 r_nbtor_refined 0.163 r_symmetry_nbd_other 0.162 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.043 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6529 Nucleic Acid Atoms Solvent Atoms 816 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing