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Protease from Norovirus Sydney GII.4 strain with crystallization epitope mutation H50Y
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 Ligand-friendly screen, condition F02
20% PEG3350
10% ethylene glycol
0.1M bis-tris-propane pH 6.5
0.2M sodium bromide
Crystal Properties Matthews coefficient Solvent content 3.84 67.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.895 α = 90 b = 128.895 β = 90 c = 118.126 γ = 120
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 EIGER2 X 16M 2023-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976269 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.41 81.132 100 0.999 10.3 42.5 43061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.45 0.413
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.411 81.132 39586 1740 92.026 0.211 0.2093 0.2092 0.252 0.2518 RANDOM 89.056
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] 1.569 0.784 1.569 -5.089
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.871 r_lrange_other 20.871 r_dihedral_angle_3_deg 19.204 r_scangle_it 17.791 r_scangle_other 17.788 r_mcangle_it 17.047 r_mcangle_other 17.045 r_dihedral_angle_6_deg 15.53 r_scbond_it 13.465 r_scbond_other 13.464
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.871 r_lrange_other 20.871 r_dihedral_angle_3_deg 19.204 r_scangle_it 17.791 r_scangle_other 17.788 r_mcangle_it 17.047 r_mcangle_other 17.045 r_dihedral_angle_6_deg 15.53 r_scbond_it 13.465 r_scbond_other 13.464 r_mcbond_it 12.699 r_mcbond_other 12.686 r_dihedral_angle_2_deg 12.336 r_dihedral_angle_1_deg 9.038 r_angle_refined_deg 2.463 r_angle_other_deg 0.946 r_symmetry_nbd_refined 0.192 r_nbd_refined 0.191 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.171 r_nbd_other 0.169 r_ncsr_local_group_4 0.159 r_ncsr_local_group_3 0.157 r_ncsr_local_group_5 0.157 r_symmetry_xyhbond_nbd_refined 0.148 r_ncsr_local_group_6 0.148 r_ncsr_local_group_2 0.144 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.122 r_ncsr_local_group_1 0.106 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5126 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing