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Structure of Sheep Polyomavirus VP1 in complex with 6'-Sialyllactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Magnesium chloride, PEG 800, TRIS
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.62 α = 90 b = 81.26 β = 115.52 c = 146.66 γ = 90
Symmetry Space Group P 1 21 1
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 2016-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 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 1.6 47.47 96.81 0.071 0.999 17.78 6.8 350203 17.04
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 1.6 1.657 0.727 0.821 2.94
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 4FMG 1.6 47.47 346733 3503 96.82 0.15197 0.15167 0.1625 0.18218 0.1916 RANDOM 18.38
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] -0.73 -0.46 0.34 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.913 r_dihedral_angle_4_deg 20.771 r_dihedral_angle_3_deg 11.426 r_dihedral_angle_1_deg 7.238 r_long_range_B_refined 4.631 r_long_range_B_other 4.631 r_scangle_other 1.813 r_mcangle_it 1.545 r_mcangle_other 1.545 r_angle_refined_deg 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.913 r_dihedral_angle_4_deg 20.771 r_dihedral_angle_3_deg 11.426 r_dihedral_angle_1_deg 7.238 r_long_range_B_refined 4.631 r_long_range_B_other 4.631 r_scangle_other 1.813 r_mcangle_it 1.545 r_mcangle_other 1.545 r_angle_refined_deg 1.51 r_angle_other_deg 1.406 r_scbond_it 1.143 r_scbond_other 1.143 r_mcbond_it 0.91 r_mcbond_other 0.909 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19623 Nucleic Acid Atoms Solvent Atoms 2753 Heterogen Atoms 366
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building