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Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with DMASPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M Bis Tris pH5.5, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.86 33.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.858 α = 90 b = 67.988 β = 90 c = 134.307 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker PHOTON III 2022-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 1.77 36.75 99.6 0.046 31.9 11.5 39950
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 0.168
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.77 36.75 37867 1959 99.45 0.15937 0.15722 0.1705 0.20163 0.2089 RANDOM 17.646
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] 0.98 -0.22 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.926 r_dihedral_angle_3_deg 12.917 r_dihedral_angle_4_deg 12.657 r_dihedral_angle_1_deg 7.627 r_long_range_B_refined 5.797 r_long_range_B_other 5.797 r_scangle_other 4.248 r_scbond_it 2.762 r_scbond_other 2.761 r_mcangle_other 2.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.926 r_dihedral_angle_3_deg 12.917 r_dihedral_angle_4_deg 12.657 r_dihedral_angle_1_deg 7.627 r_long_range_B_refined 5.797 r_long_range_B_other 5.797 r_scangle_other 4.248 r_scbond_it 2.762 r_scbond_other 2.761 r_mcangle_other 2.284 r_mcangle_it 2.282 r_angle_refined_deg 1.707 r_mcbond_it 1.52 r_mcbond_other 1.503 r_angle_other_deg 1.458 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 3096 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SAINT data scaling PHASER phasing