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BK Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aromatic linker)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH 7.5, 0.25 M LiCl, 18% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.327 α = 90 b = 151.838 β = 90 c = 63.052 γ = 90
Symmetry Space Group P 21 21 2
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 1.9 48.5 99.9 0.19 0.99 12.84 13.42 110045
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 2.01 1.94 0.61
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 4MJ1 1.9 48.5 110045 3302 99.884 0.189 0.1874 0.1953 0.2262 0.2319 30.528
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] 1.487 0.003 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.367 r_dihedral_angle_4_deg 21.075 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_1_deg 7.441 r_lrange_it 5.893 r_lrange_other 5.892 r_scangle_it 4.552 r_scangle_other 4.552 r_mcangle_it 3.461 r_mcangle_other 3.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.367 r_dihedral_angle_4_deg 21.075 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_1_deg 7.441 r_lrange_it 5.893 r_lrange_other 5.892 r_scangle_it 4.552 r_scangle_other 4.552 r_mcangle_it 3.461 r_mcangle_other 3.461 r_scbond_it 3.073 r_scbond_other 3.072 r_mcbond_it 2.417 r_mcbond_other 2.416 r_angle_other_deg 2.384 r_angle_refined_deg 1.492 r_nbd_other 0.28 r_symmetry_xyhbond_nbd_refined 0.237 r_symmetry_nbd_refined 0.222 r_symmetry_nbd_other 0.21 r_nbd_refined 0.199 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.099 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_bond_other_d 0.036 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9838 Nucleic Acid Atoms Solvent Atoms 748 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing