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Structure of Human Polyomavirus 9 VP1 pentamer in complex with N-glycolylneuraminic acid containing 3'-sialyllactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4POQ PDB ENTRY 4POQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.15 293 20% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM (N-glycolyl neuraminic acid) 3'-sialyllactosamine for 20 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.02 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.4 α = 90 b = 177.65 β = 90 c = 198.65 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors 2012-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 132.422 99.4 0.15 10.52 3.84 211585 212860 -3 -3 28.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 99.65 0.81 2.25 3.98 15585
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4POQ 2.1 132.422 211585 201037 10548 99.31 0.18595 0.18595 0.18394 0.186 0.22428 0.2257 RANDOM 26.366
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] 0.07 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 18.154 r_dihedral_angle_3_deg 12.92 r_dihedral_angle_1_deg 6.167 r_long_range_B_refined 5.481 r_angle_refined_deg 1.222 r_mcangle_it 1.171 r_scbond_it 1.127 r_mcbond_it 0.673 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 18.154 r_dihedral_angle_3_deg 12.92 r_dihedral_angle_1_deg 6.167 r_long_range_B_refined 5.481 r_angle_refined_deg 1.222 r_mcangle_it 1.171 r_scbond_it 1.127 r_mcbond_it 0.673 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20595 Nucleic Acid Atoms Solvent Atoms 2395 Heterogen Atoms 636
Software Software Software Name Purpose RemDAq data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling