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Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YLA PDB entries 1YLA and 1A3S experimental model PDB 1A3S PDB entries 1YLA and 1A3S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.07 59.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.874 α = 85.05 b = 68.498 β = 80.85 c = 91.277 γ = 75.83
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2006-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.91841 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 30 93.3 0.051 13.9 1.9 27651 27651 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 70.8 0.293 2.17 1.7 1028
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entries 1YLA and 1A3S 2.6 30 27651 26281 1398 92.92 0.23105 0.22775 0.2189 0.29091 0.279 RANDOM 34.036
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] -2.31 0.79 1.94 -2.91 -1.17 4.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.074 r_dihedral_angle_3_deg 20.218 r_dihedral_angle_4_deg 14.615 r_dihedral_angle_1_deg 5.437 r_scangle_it 1.693 r_angle_refined_deg 1.624 r_scbond_it 1.068 r_mcangle_it 0.636 r_mcbond_it 0.4 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.074 r_dihedral_angle_3_deg 20.218 r_dihedral_angle_4_deg 14.615 r_dihedral_angle_1_deg 5.437 r_scangle_it 1.693 r_angle_refined_deg 1.624 r_scbond_it 1.068 r_mcangle_it 0.636 r_mcbond_it 0.4 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.1 r_symmetry_hbond_refined 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5628 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing