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Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 20% PEG 10000, 8% Ethylene glycol, 0.1M HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.696 α = 90 b = 47.415 β = 118.32 c = 67.975 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2010-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.58 50 99.7 0.033 23 6.2 39104 38987 22.22
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) 1 1.58 1.64 96.9 0.289 5.296 4.8 3797
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT 5D1K 1.581 30.398 1.34 40696 38983 1000 95.79 0.1891 0.1882 0.1858 0.2231 0.2211 RANDOM 27.7522
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] -4.684 -0.2176 7.9872 -3.9489
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.09 f_angle_d 1.175 f_chiral_restr 0.085 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2068 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 23
Software Software Software Name Purpose HKL-3000 data reduction PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data scaling PHENIX phasing