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GII.10 human norovirus protruding domain in complex with glycochenodeoxycholate (GCDCA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ONU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0,1M Magnesium acetate tetrahydrate
0,1M Sodium citrate pH 5.8
14% w/v PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.85 α = 90 b = 79.67 β = 90 c = 87.69 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 6M 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.972640 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 45.93 99.38 0.06655 0.07248 0.02835 0.999 16.89 6.4 60120 28.15
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 1.9 1.97 96.4 0.6555 0.7159 0.2838 0.8 2.49 6.2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ONU 1.9 45.93 1.36 60113 3006 99.39 0.1667 0.1654 0.1665 0.1899 0.1902
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 11.826 f_angle_d 0.75 f_chiral_restr 0.053 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4708 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing