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X-ray structure of Triatoma virus empty capsid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 Crystal were growth at 291.15 K by vapor diffusion in sitting drop plates mixing equal volumes of the capsid solution at 3 mg/mL and of the reservoir solution: 100 mM Tris pH 8.5, 50 mM MgCl2 and 25% pentaerythritol propoxilate 629.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 305.586 α = 90 b = 305.586 β = 90 c = 796.486 γ = 120
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 PILATUS3 6M 2015-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9795 ESRF ID23-1
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 3.6 49.91 98 0.162 5.17 2.2 315756
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 3.6 3.7 97 2.2
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 3NAP 3.6 49.91 309319 6432 98.28 0.26874 0.26873 0.2703 0.26917 0.2695 RANDOM 113.221
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] 0.54 0.27 0.54 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_3_deg 15.613 r_dihedral_angle_4_deg 13.953 r_long_range_B_refined 11.048 r_long_range_B_other 11.047 r_scangle_other 7.875 r_dihedral_angle_1_deg 7.395 r_mcangle_it 6.333 r_mcangle_other 6.332 r_scbond_it 4.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_3_deg 15.613 r_dihedral_angle_4_deg 13.953 r_long_range_B_refined 11.048 r_long_range_B_other 11.047 r_scangle_other 7.875 r_dihedral_angle_1_deg 7.395 r_mcangle_it 6.333 r_mcangle_other 6.332 r_scbond_it 4.506 r_scbond_other 4.505 r_mcbond_it 3.858 r_mcbond_other 3.858 r_angle_refined_deg 1.159 r_angle_other_deg 0.719 r_chiral_restr 0.062 r_bond_refined_d 0.007 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 5398 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing