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Sheep Polyomavirus VP1 in complex with 10 mM globo-N-tetraose
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 3.56 65.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.274 α = 90 b = 130.274 β = 90 c = 222.145 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 2019-12-13 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 1.7 48.91 99.9 0.107 0.998 13.51 5.78 462792 27.9
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 1.7 1.8 1.085 0.485 1.61
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 1.701 48.908 458240 4550 99.951 0.144 0.1433 0.1493 0.1651 0.1704 22.373
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] -2.032 -2.032 4.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.195 r_dihedral_angle_4_deg 24.061 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_1_deg 7.446 r_lrange_it 5.153 r_lrange_other 4.854 r_scangle_it 2.983 r_scangle_other 2.983 r_angle_other_deg 2.543 r_mcangle_it 2.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.195 r_dihedral_angle_4_deg 24.061 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_1_deg 7.446 r_lrange_it 5.153 r_lrange_other 4.854 r_scangle_it 2.983 r_scangle_other 2.983 r_angle_other_deg 2.543 r_mcangle_it 2.493 r_mcangle_other 2.493 r_scbond_it 2.087 r_scbond_other 2.086 r_mcbond_it 1.727 r_mcbond_other 1.727 r_angle_refined_deg 1.635 r_metal_ion_refined 0.275 r_nbd_other 0.272 r_symmetry_nbd_other 0.216 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.072 r_bond_other_d 0.036 r_gen_planes_other 0.015 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20328 Nucleic Acid Atoms Solvent Atoms 3203 Heterogen Atoms 411
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building