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Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with DMAPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZXK 5ZXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M Bis Tris pH 5.5, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.24 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.172 α = 90 b = 67.895 β = 90 c = 134.622 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 2022-03-13 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 1.8 37.06 99.9 0.0898 15.45 11.14 38449
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 1.8 1.83 0.3514
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 5ZXK 1.8 37.05 36385 1943 99.8 0.1724 0.17 0.1809 0.2163 0.2238 RANDOM 21.138
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] 1.16 -0.28 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.417 r_dihedral_angle_4_deg 15.109 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 7.755 r_angle_refined_deg 1.625 r_angle_other_deg 1.407 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.417 r_dihedral_angle_4_deg 15.109 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 7.755 r_angle_refined_deg 1.625 r_angle_other_deg 1.407 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3096 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 29
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction PHASER phasing