☰ Navigation Tabs
Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FMG PDB entry 4FMG
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
Crystal Properties Matthews coefficient Solvent content 2.29 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.1 α = 90 b = 153.64 β = 91.83 c = 143.98 γ = 90
Symmetry Space Group P 1 21 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 PIXEL PSI PILATUS 6M 2011-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 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 2.1 30 98.3 12 4.7 158871 44.1
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 2.1 2.16 92.8 1.7 4.4
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 PDB entry 4FMG 2.1 29.57 150901 7970 98.31 0.20682 0.20458 0.2074 0.24916 0.2481 RANDOM 42.085
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] 30.05 -10.12 5.74 -35.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.344 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_1_deg 6.263 r_long_range_B_other 5.96 r_long_range_B_refined 5.958 r_scangle_other 4.452 r_scbond_it 3.635 r_scbond_other 3.635 r_mcangle_it 3.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.344 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_1_deg 6.263 r_long_range_B_other 5.96 r_long_range_B_refined 5.958 r_scangle_other 4.452 r_scbond_it 3.635 r_scbond_other 3.635 r_mcangle_it 3.441 r_mcangle_other 3.441 r_mcbond_it 2.914 r_mcbond_other 2.914 r_angle_refined_deg 1.273 r_angle_other_deg 0.733 r_chiral_restr 0.076 r_bond_refined_d 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20369 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data reduction Coot model building XSCALE data scaling