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Crystal structure of the Zn-bound ubiquitin-conjugating enzyme Ube2T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% PEG3350, 0.2 M calcium acetate, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.02 α = 90 b = 96.383 β = 93.28 c = 89.996 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 DECTRIS PILATUS 2M 2016-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 48.75 99.7 0.038 0.998 16.6 3.4 81137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 99.6 0.292 0.849 3.1 3.1
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 1YH2 1.85 48.75 77077 4035 99.64 0.17915 0.17809 0.1868 0.19885 0.207 RANDOM 28.966
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] 0.06 -0.24 0.7 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 16.064 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 6.372 r_long_range_B_refined 5.941 r_long_range_B_other 5.908 r_scangle_other 3.513 r_mcangle_other 2.683 r_mcangle_it 2.682 r_scbond_it 2.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 16.064 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 6.372 r_long_range_B_refined 5.941 r_long_range_B_other 5.908 r_scangle_other 3.513 r_mcangle_other 2.683 r_mcangle_it 2.682 r_scbond_it 2.171 r_scbond_other 2.171 r_mcbond_it 1.722 r_mcbond_other 1.718 r_angle_refined_deg 1.474 r_angle_other_deg 0.965 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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 7215 Nucleic Acid Atoms Solvent Atoms 978 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing