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JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aliphatic 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% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.098 α = 90 b = 96.023 β = 110.555 c = 128.058 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 1.24 48.012 95.9 0.07 0.99 12.14 4.78 464154
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 1.24 1.31 1.04 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 1.24 48.012 463097 9262 95.983 0.138 0.1375 0.1443 0.1547 0.1612 16.372
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] -0.48 0.104 -0.136 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.985 r_dihedral_angle_4_deg 17.667 r_dihedral_angle_3_deg 12.208 r_rigid_bond_restr 11.366 r_dihedral_angle_1_deg 7.383 r_lrange_it 3.953 r_lrange_other 3.201 r_scangle_it 2.657 r_scangle_other 2.657 r_angle_other_deg 2.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.985 r_dihedral_angle_4_deg 17.667 r_dihedral_angle_3_deg 12.208 r_rigid_bond_restr 11.366 r_dihedral_angle_1_deg 7.383 r_lrange_it 3.953 r_lrange_other 3.201 r_scangle_it 2.657 r_scangle_other 2.657 r_angle_other_deg 2.476 r_scbond_it 2.195 r_scbond_other 2.195 r_mcangle_it 1.769 r_mcangle_other 1.769 r_angle_refined_deg 1.659 r_mcbond_it 1.423 r_mcbond_other 1.423 r_nbd_refined 0.229 r_symmetry_nbd_other 0.225 r_symmetry_nbd_refined 0.214 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.169 r_nbd_other 0.168 r_symmetry_xyhbond_nbd_refined 0.164 r_metal_ion_refined 0.118 r_symmetry_xyhbond_nbd_other 0.103 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_bond_other_d 0.035 r_gen_planes_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10070 Nucleic Acid Atoms Solvent Atoms 1965 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing