☰ Navigation Tabs
Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 6'-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 3.5 64.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.645 α = 90 b = 129.645 β = 90 c = 220.431 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 1.9 49.48 99.8 0.1461 0.996 9.46 5.3 325151 31.3
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 1.9 2.02 1.223 0.441 1.33
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 1.901 49.47 321986 3164 99.764 0.1461 0.1461 0.151 0.1726 0.177 26.683
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] -5.055 -5.055 10.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_4_deg 22.319 r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 7.94 r_lrange_it 4.796 r_lrange_other 4.687 r_scangle_it 3.338 r_scangle_other 3.338 r_mcangle_other 2.892 r_mcangle_it 2.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_4_deg 22.319 r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 7.94 r_lrange_it 4.796 r_lrange_other 4.687 r_scangle_it 3.338 r_scangle_other 3.338 r_mcangle_other 2.892 r_mcangle_it 2.891 r_angle_other_deg 2.744 r_scbond_it 2.42 r_scbond_other 2.42 r_mcbond_it 2.124 r_mcbond_other 2.123 r_angle_refined_deg 1.65 r_nbd_other 0.271 r_symmetry_nbd_other 0.217 r_symmetry_xyhbond_nbd_refined 0.184 r_symmetry_nbd_refined 0.179 r_nbd_refined 0.178 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbtor_other 0.096 r_chiral_restr 0.079 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 20381 Nucleic Acid Atoms Solvent Atoms 2023 Heterogen Atoms 893
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building