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BK Polyomavirus VP1 pentamer in complex with GD3 oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native BK Polyomavirus VP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 16-18 % PEG 3,350, 0.1 M HEPES pH 7.5, 0.25 M LiCl , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.68 α = 90 b = 152.64 β = 90 c = 63.19 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 100 PIXEL PSI PILATUS 6M 2009-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 100 19.44 7.2 154229 154169 -3 -3 26.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 99.8 2.66 5.7 11266
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 native BK Polyomavirus VP1 1.7 48 154166 148771 5395 99.96 0.15064 0.15064 0.14969 0.1557 0.1769 0.1791 RANDOM 17.115
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_4_deg 21.083 r_dihedral_angle_3_deg 11.807 r_dihedral_angle_1_deg 6.286 r_scangle_it 3.388 r_scbond_it 2.336 r_mcangle_it 1.877 r_angle_refined_deg 1.311 r_mcbond_it 1.254 r_angle_other_deg 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_4_deg 21.083 r_dihedral_angle_3_deg 11.807 r_dihedral_angle_1_deg 6.286 r_scangle_it 3.388 r_scbond_it 2.336 r_mcangle_it 1.877 r_angle_refined_deg 1.311 r_mcbond_it 1.254 r_angle_other_deg 0.829 r_mcbond_other 0.591 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 10008 Nucleic Acid Atoms Solvent Atoms 1280 Heterogen Atoms 244
Software Software Software Name Purpose RemDAq data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling