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Sheep Polyomavirus VP1 in complex with 10 mM Forssman antigen pentaose
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 3.58 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.494 α = 90 b = 130.494 β = 90 c = 222.435 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 2019-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0077 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 1.85 42.72 99.8 0.105 0.998 14.42 6.75 361163 32.4
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 1.85 1.96 98.8 1.045 0.99 1.77 6.01
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 1.923 42.714 317860 3205 99.782 0.15 0.1493 0.1545 0.1757 0.1803 28.073
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] -7.491 -7.491 14.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 20.32 r_dihedral_angle_3_deg 12.475 r_dihedral_angle_1_deg 7.724 r_lrange_it 5.116 r_lrange_other 4.948 r_scangle_it 3.607 r_scangle_other 3.607 r_mcangle_it 3.078 r_mcangle_other 3.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 20.32 r_dihedral_angle_3_deg 12.475 r_dihedral_angle_1_deg 7.724 r_lrange_it 5.116 r_lrange_other 4.948 r_scangle_it 3.607 r_scangle_other 3.607 r_mcangle_it 3.078 r_mcangle_other 3.078 r_scbond_it 2.625 r_scbond_other 2.625 r_angle_other_deg 2.582 r_mcbond_it 2.301 r_mcbond_other 2.3 r_angle_refined_deg 1.643 r_nbd_other 0.272 r_symmetry_nbd_other 0.213 r_symmetry_nbd_refined 0.2 r_nbd_refined 0.187 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.075 r_bond_other_d 0.035 r_metal_ion_refined 0.015 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 20397 Nucleic Acid Atoms Solvent Atoms 2235 Heterogen Atoms 725
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building