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Crystallographic structure of human Tsg101 UEV domain in complex with a HEV ORF3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 288 0.1M Citric Acid, 2M Ammonium sulfate pH 3.5, 13.34% glycerol
Crystal Properties Matthews coefficient Solvent content 2.4 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.57 α = 90 b = 42.57 β = 90 c = 188.16 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 9M 2020-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980108 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.398 47.084 100 1 23.7 4.6 35532
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 0.875
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3OBQ 1.398 47.084 35531 1777 99.952 0.221 0.2199 0.239 0.2421 24.312
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] 0.244 0.244 -0.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.864 r_dihedral_angle_4_deg 23.385 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 6.282 r_angle_refined_deg 1.786 r_angle_other_deg 1.374 r_symmetry_nbd_refined 0.319 r_nbd_refined 0.23 r_nbd_other 0.227 r_nbtor_refined 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.864 r_dihedral_angle_4_deg 23.385 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 6.282 r_angle_refined_deg 1.786 r_angle_other_deg 1.374 r_symmetry_nbd_refined 0.319 r_nbd_refined 0.23 r_nbd_other 0.227 r_nbtor_refined 0.193 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.137 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1210 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling MOLREP phasing