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Structure of Human Polyomavirus 7 (HPyV7) VP1 pentamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S7X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 100 mM Na-Malonate pH 4.5, 15% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.67 α = 90 b = 86.43 β = 92.14 c = 84.21 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 100 CCD MARMOSAIC 225 mm CCD 2010-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9795 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 1.7 30 97.8 15.7 3.9 161009 -3 26
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 1.75 82.1 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3S7X 1.7 30 152915 8094 97.78 0.17067 0.1693 0.19662 0.1911 RANDOM 24.71
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] 0.33 0.35 0.06 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.909 r_dihedral_angle_4_deg 17.297 r_dihedral_angle_3_deg 12.132 r_long_range_B_refined 6.27 r_long_range_B_other 6.269 r_dihedral_angle_1_deg 6.189 r_scangle_other 3.718 r_scbond_it 2.799 r_scbond_other 2.799 r_mcangle_it 2.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.909 r_dihedral_angle_4_deg 17.297 r_dihedral_angle_3_deg 12.132 r_long_range_B_refined 6.27 r_long_range_B_other 6.269 r_dihedral_angle_1_deg 6.189 r_scangle_other 3.718 r_scbond_it 2.799 r_scbond_other 2.799 r_mcangle_it 2.199 r_mcangle_other 2.199 r_mcbond_it 1.707 r_mcbond_other 1.702 r_angle_refined_deg 1.39 r_angle_other_deg 0.759 r_chiral_restr 0.082 r_bond_refined_d 0.01 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 9689 Nucleic Acid Atoms Solvent Atoms 990 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHENIX refinement PHASER phasing Coot model building