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Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1 oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 100 mM Na-malonate pH 5.0, 10% PEG 3350, 10 mM GM1 oligosaccharide
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.99 α = 90 b = 152.05 β = 90 c = 67.97 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 DECTRIS PILATUS 2M 2012-03-15 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) 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 1.5 50 99.4 16 5.5 238315 21.5
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 1.5 1.54 99 5.3
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 (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 4U5Z 1.5 50 226492 11948 99.43 0.15874 0.15764 0.1575 0.17994 0.1801 RANDOM 17.962
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] 0.02 -0.38 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 11.352 r_dihedral_angle_1_deg 6.136 r_long_range_B_refined 5.75 r_long_range_B_other 5.75 r_angle_refined_deg 1.419 r_scangle_other 1.344 r_scbond_it 0.887 r_scbond_other 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 11.352 r_dihedral_angle_1_deg 6.136 r_long_range_B_refined 5.75 r_long_range_B_other 5.75 r_angle_refined_deg 1.419 r_scangle_other 1.344 r_scbond_it 0.887 r_scbond_other 0.886 r_angle_other_deg 0.83 r_mcangle_it 0.797 r_mcangle_other 0.797 r_mcbond_it 0.48 r_mcbond_other 0.479 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10436 Nucleic Acid Atoms Solvent Atoms 1637 Heterogen Atoms 323
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data reduction Coot model building XSCALE data scaling