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The structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) essential for Leishmania amastigote differentiation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J7D PDB ID: 1J7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 UBC2 and UEV1 were mixed in a 1:1 molar ratio to a final concentration of 6.6 mg mL-1 and incubated on ice for 30 min. Crystals were grown using a sitting drop method with a 1:1 ratio of protein to reservoir solution (0.1 M Bis-Tris propane, pH 7.5, 0.2 M sodium formate and 20% PEG) in the drop. Crystals took 2 days to appear.
Crystal Properties Matthews coefficient Solvent content 2.16 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.523 α = 90 b = 72.568 β = 91.839 c = 120.094 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 EIGER2 XE 16M 2019-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976254 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.65 47.25 100 0.092 0.12 0.075 0.996 6.7 4.2 67149
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 1.449 1.635 0.747 0.368 4.2
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB ID: 1J7D 1.7 46.25 61440 3018 99.964 0.225 0.2228 0.2603 0.2903 31.043
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] 1.251 -1.504 0.342 -1.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 16.923 r_dihedral_angle_3_deg 16.909 r_dihedral_angle_1_deg 6.887 r_lrange_it 6.373 r_scangle_it 4.981 r_mcangle_it 3.658 r_scbond_it 3.458 r_mcbond_it 2.644 r_angle_refined_deg 1.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 16.923 r_dihedral_angle_3_deg 16.909 r_dihedral_angle_1_deg 6.887 r_lrange_it 6.373 r_scangle_it 4.981 r_mcangle_it 3.658 r_scbond_it 3.458 r_mcbond_it 2.644 r_angle_refined_deg 1.564 r_nbtor_refined 0.315 r_symmetry_xyhbond_nbd_refined 0.283 r_symmetry_nbd_refined 0.21 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.115 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4622 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction Aimless data scaling MOLREP phasing