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Crystal structure of capsid P domain of norovirus GI.3 VA115
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 0.2M Sodium formate pH 6.4, 17% (w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.275 α = 101.89 b = 60.001 β = 97.73 c = 92.368 γ = 110.1
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 RIGAKU SATURN 944 2018-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.183 50 94.1 0.076 0.085 0.036 15.5 5.4 54367
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 2.2 2.24 67.9 0.354 0.408 0.198 0.951 3.7
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4P25 2.183 41.78 51267 2841 92.91 0.188 0.1859 0.226 0.2145 RANDOM 18.069
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] 1.14 -0.63 -1.77 0.05 -0.18 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.215 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_3_deg 12.229 r_dihedral_angle_1_deg 7.746 r_angle_refined_deg 1.325 r_angle_other_deg 1.178 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.215 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_3_deg 12.229 r_dihedral_angle_1_deg 7.746 r_angle_refined_deg 1.325 r_angle_other_deg 1.178 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9227 Nucleic Acid Atoms Solvent Atoms 1085 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing