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1.85A resolution structure of Norovirus 3CL protease complex with a covalently bound dipeptidyl inhibitor diethyl [(1R,2S)-2-[(N-{[(3-chlorobenzyl)oxy]carbonyl}-3-cyclohexyl-L-alanyl)amino]-1-hydroxy-3-(2-oxo-2H-pyrrol-3-yl)propyl]phosphonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 20% (w/v) PEG 5000 MME, 100 mM Tris, 200 mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.171 α = 90 b = 124.171 β = 90 c = 49.969 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 PILATUS 6M 2014-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 45.32 100 0.197 0.998 14.9 19.3 19899 18.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 100 1.505 0.763 2.4 18.5 1197
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3UR9 1.85 45.316 1.24 19875 968 99.99 0.1641 0.1625 0.1771 0.1965 0.2079 RANDOM 21.1897
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 13.635 f_angle_d 1.229 f_chiral_restr 0.254 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1218 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 38
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data scaling