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Crystal structure of capsid P domain of norovirus GI.3 VA115 complexed with Gala1-3Galb1-4Glc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ER0
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 1.99 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.29 α = 102.28 b = 59.637 β = 96.72 c = 91.419 γ = 109.77
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 2021-02-09 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 2.2 50 94.5 0.081 0.092 0.042 11 4.5 52013
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 73.4 0.161 0.186 0.091 0.978 3.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7ER0 2.2 41.29 49385 2621 93.43 0.1802 0.1781 0.1843 0.2198 0.2219 RANDOM 24.354
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] 2.07 -0.7 -3.22 -0.79 -0.67 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.483 r_dihedral_angle_4_deg 17.025 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 7.567 r_angle_refined_deg 1.321 r_angle_other_deg 1.149 r_chiral_restr 0.05 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 34.483 r_dihedral_angle_4_deg 17.025 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 7.567 r_angle_refined_deg 1.321 r_angle_other_deg 1.149 r_chiral_restr 0.05 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 9203 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing