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Crystal structure of a complex between the E2 conjugating enzyme UBE2A and the E3 ligase module from UBR4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277 0.1 M Bis-Tris, pH 6.4, 15% PEG10000, 0.2 M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.157 α = 90 b = 89.157 β = 90 c = 263.306 γ = 90
Symmetry Space Group P 43 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 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9118 Diamond I04-1
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 3.2 65.83 99.62 0.997 8.04 12.5 18375
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 3.2 3.315 99.5 0.934 1.35 13.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.2 65.83 1.34 18310 970 99.63 0.23 0.2282 0.232 0.2625 0.2548 82.05
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.5704 f_angle_d 0.4398 f_chiral_restr 0.038 f_plane_restr 0.0038 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5186 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing