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Structure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other wild-type structure of Hemagglutinin-esterase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.04 M KH2PO4, 16% (w/v) PEG 8000, 20% (w/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.78 67.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.24 α = 90 b = 89.24 β = 90 c = 280.38 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 CCD ADSC QUANTUM 315 2006-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 77.4 97.2 0.092 25.5 20.7 60345 60283 -3.7 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 86.6 0.866 3.5 19 7667
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 wild-type structure of Hemagglutinin-esterase 1.8 50 57018 57018 3043 96.05 0.1712 0.17031 0.1815 0.1883 0.2022 RANDOM 25.046
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] 0.28 0.14 0.28 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.994 r_dihedral_angle_4_deg 15.925 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_1_deg 6.754 r_scangle_it 2.974 r_scbond_it 1.858 r_angle_refined_deg 1.334 r_angle_other_deg 1.282 r_mcangle_it 1.134 r_mcbond_it 0.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.994 r_dihedral_angle_4_deg 15.925 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_1_deg 6.754 r_scangle_it 2.974 r_scbond_it 1.858 r_angle_refined_deg 1.334 r_angle_other_deg 1.282 r_mcangle_it 1.134 r_mcbond_it 0.625 r_mcbond_other 0.164 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2860 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement DNA data collection XDS data reduction SCALA data scaling PHASER phasing