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Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to A trisaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SJP PDB ENTRY 3SJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295.15 0.8M potassium sodium tartarate, 100mM Tris, 0.5% w/v PEG monomethyl ether 5000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K
Crystal Properties Matthews coefficient Solvent content 3.79 67.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 244.537 α = 90 b = 341.456 β = 90 c = 124.772 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315r 2010-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.67 50 99.4 0.106 0.096 12.68 5.5 144302 143411 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.72 99.4 0.404 0.377 2.35 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3SJP 2.679 41.655 136204 136204 7204 98.13 0.18343 0.18098 0.1864 0.23029 0.2315 RANDOM 37.117
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] -0.89 -0.34 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_4_deg 21.323 r_dihedral_angle_3_deg 16.788 r_dihedral_angle_1_deg 7.368 r_scangle_it 4.437 r_scbond_it 2.674 r_angle_refined_deg 1.986 r_mcangle_it 1.787 r_mcbond_it 0.936 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_4_deg 21.323 r_dihedral_angle_3_deg 16.788 r_dihedral_angle_1_deg 7.368 r_scangle_it 4.437 r_scbond_it 2.674 r_angle_refined_deg 1.986 r_mcangle_it 1.787 r_mcbond_it 0.936 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23612 Nucleic Acid Atoms Solvent Atoms 707 Heterogen Atoms 288
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling