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Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, sodium maolante
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.277 α = 90 b = 146.16 β = 90 c = 150.413 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 2M-F 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.98 49.05 99.8 0.29 0.995 8.52 10.5 212141 28.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.1 98.7 1.56 0.65 1.76 10.8
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 4U60 1.98 49.05 210019 2122 99.76 0.1852 0.1847 0.2299 0.2058 RANDOM 26.585
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] -0.27 -1.55 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.899 r_dihedral_angle_4_deg 18.499 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 6.85 r_angle_refined_deg 1.301 r_angle_other_deg 0.881 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.899 r_dihedral_angle_4_deg 18.499 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 6.85 r_angle_refined_deg 1.301 r_angle_other_deg 0.881 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20664 Nucleic Acid Atoms Solvent Atoms 2360 Heterogen Atoms 215
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing PDB_EXTRACT data extraction XDS data scaling