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Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 3'-sialyllactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 KSCN, PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.55 65.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.404 α = 90 b = 130.404 β = 90 c = 221.221 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 2M-F 2019-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 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 1.798 48.85 99.8 0.162 0.997 11.02 9.9 390469 28.5
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 1.8 1.91 1.273 0.471 1.51
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Y61 1.798 48.846 390439 6588 99.8 0.153 0.1521 0.156 0.177 0.181 24.646
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] 0.211 0.211 -0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.663 r_dihedral_angle_4_deg 21.198 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 7.932 r_lrange_it 4.512 r_lrange_other 4.362 r_scangle_it 2.969 r_scangle_other 2.969 r_angle_other_deg 2.861 r_mcangle_it 2.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.663 r_dihedral_angle_4_deg 21.198 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 7.932 r_lrange_it 4.512 r_lrange_other 4.362 r_scangle_it 2.969 r_scangle_other 2.969 r_angle_other_deg 2.861 r_mcangle_it 2.764 r_mcangle_other 2.763 r_scbond_it 2.153 r_scbond_other 2.153 r_mcbond_it 2.036 r_mcbond_other 2.036 r_angle_refined_deg 1.721 r_nbd_other 0.276 r_symmetry_nbd_other 0.216 r_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.165 r_metal_ion_refined 0.152 r_symmetry_nbd_refined 0.121 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.068 r_bond_other_d 0.035 r_gen_planes_other 0.014 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20301 Nucleic Acid Atoms Solvent Atoms 2352 Heterogen Atoms 665
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building