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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 malonate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.4 α = 90 b = 145.705 β = 90 c = 149.453 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 2017-11-27 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 1.75 47.95 99.97 0.11 0.999 15.72 8.7 302337 26.26
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 1.75 1.81 99.9 1.78 0.48 1.29 9
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 4u60 1.75 47.95 299628 3027 99.82 0.1761 0.1759 0.1842 0.201 0.2072 RANDOM 28.649
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] 0.28 -0.68 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.369 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 6.859 r_angle_refined_deg 1.302 r_angle_other_deg 0.938 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.369 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 6.859 r_angle_refined_deg 1.302 r_angle_other_deg 0.938 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20567 Nucleic Acid Atoms Solvent Atoms 2873 Heterogen Atoms 285
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction XDS data scaling PHASER phasing