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Enterovirus 71 Polymerase Elongation Complex with a remdesivir nucleotide at product strand positions +1 (C1S5 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 289 0.08 M sodium acetate pH 5.0
1.6 M ammonion sulfate
20% (vol./vol.) glycerol
Crystal Properties Matthews coefficient Solvent content 3.09 60.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.643 α = 90 b = 77.643 β = 90 c = 490.226 γ = 120
Symmetry Space Group P 65 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 EIGER X 16M 2020-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
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 2.7 50 95.3 0.087 0.093 0.032 0.997 9.9 8.9 24429
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 2.7 2.8 100 0.695 0.728 0.216 0.914 11.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.7 37.77 1.35 24221 1236 94.81 0.2189 0.2173 0.2173 0.2493 0.2496 87.04
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 9.324 f_angle_d 1.0288 f_chiral_restr 0.0545 f_plane_restr 0.0086 f_bond_d 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3613 Nucleic Acid Atoms 614 Solvent Atoms 2 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data scaling PHENIX phasing HKL-2000 data reduction