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Structure of Sheep Polyomavirus VP1 in complex with 3'-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, HANGING DROP 293.15 KSCN, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.286 α = 90 b = 79.93 β = 116 c = 145.884 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 2019-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999 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 1.651 48.81 99.82 0.1012 0.999 13.87 6.8 322288
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 1.651 1.71 1.547 0.471 1.22
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 4FMG 1.651 48.807 322280 7413 99.827 0.17 0.1689 0.1779 0.1999 0.2071 21.746
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] -0.433 -0.827 0.814 0.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.482 r_dihedral_angle_4_deg 24.253 r_dihedral_angle_3_deg 11.774 r_dihedral_angle_1_deg 7.375 r_lrange_it 4.74 r_lrange_other 4.52 r_scangle_it 2.918 r_scangle_other 2.918 r_mcangle_it 2.135 r_mcangle_other 2.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.482 r_dihedral_angle_4_deg 24.253 r_dihedral_angle_3_deg 11.774 r_dihedral_angle_1_deg 7.375 r_lrange_it 4.74 r_lrange_other 4.52 r_scangle_it 2.918 r_scangle_other 2.918 r_mcangle_it 2.135 r_mcangle_other 2.135 r_scbond_it 1.882 r_scbond_other 1.881 r_angle_refined_deg 1.481 r_mcbond_it 1.419 r_mcbond_other 1.418 r_angle_other_deg 1.331 r_symmetry_nbd_refined 0.278 r_nbd_other 0.217 r_symmetry_nbd_other 0.192 r_nbd_refined 0.19 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.076 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19601 Nucleic Acid Atoms Solvent Atoms 2308 Heterogen Atoms 357
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building