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Crystal structure of the U-box domain of human ubiquitin-protein ligase (E3), NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR4604D.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.8 293 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1% w/v (+-)-2-methyl-2,4-pentanediol, 0.1% w/v 1,2,3-heptanetriol, 0.1% w/v dirthylenetriaminepentakis (methylphosphonic acid), 0.1% w/v D-Sorbitol, 0.1% w/v glycerol, 0.06M HEPES sodium, 12.5% PEG3350, microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.544 α = 90 b = 34.922 β = 90.78 c = 86.709 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 CCD ADSC QUANTUM 270 2010-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9789 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.292 30 99.4 0.079 28.6 5.5 38061 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 98.7 0.444 5.1 5.5
Refinement Statistics Diffraction ID Structure Solution 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 SAD 2.292 28.005 0.04 36218 1843 94.87 0.1925 0.1897 0.1851 0.2449 0.2383 52.249
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 19.512 f_angle_d 1.149 f_chiral_restr 0.076 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2713 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SnB phasing REFMAC refinement