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JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aromatic linker)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.9 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.146 α = 90 b = 96.635 β = 110.487 c = 128.555 γ = 90
Symmetry Space Group C 1 2 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 2022-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99 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 1.55 44.8 95.9 0.1 0.99 10.61 4.74 248912
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 1.55 1.64 1.3 0.49
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 3NXD 1.55 44.8 248910 4979 99.791 0.167 0.167 0.1796 0.1909 0.2033 18.833
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] -0.555 -0.116 -0.02 0.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.688 r_dihedral_angle_4_deg 17.539 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 7.158 r_lrange_it 5.6 r_lrange_other 5.168 r_scangle_it 3.285 r_scangle_other 3.285 r_angle_other_deg 2.396 r_mcangle_other 2.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.688 r_dihedral_angle_4_deg 17.539 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 7.158 r_lrange_it 5.6 r_lrange_other 5.168 r_scangle_it 3.285 r_scangle_other 3.285 r_angle_other_deg 2.396 r_mcangle_other 2.095 r_mcangle_it 2.094 r_scbond_it 2.072 r_scbond_other 2.072 r_angle_refined_deg 1.502 r_mcbond_it 1.329 r_mcbond_other 1.326 r_symmetry_nbd_other 0.213 r_nbd_refined 0.203 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_nbd_refined 0.14 r_symmetry_xyhbond_nbd_other 0.099 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.074 r_bond_other_d 0.036 r_gen_planes_other 0.013 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10099 Nucleic Acid Atoms Solvent Atoms 1703 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing