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Crystal structure of human OTUB1/UbcH5b~Ub/Ub
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ESK PDB ENTRY 2ESK AND 2ZFY experimental model PDB 2ZFY PDB ENTRY 2ESK AND 2ZFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.566 α = 90 b = 104.928 β = 104.19 c = 148.479 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 198.25 CCD RAYONIX MX-300 2011-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2987 49.29 99.54 60666 60387
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2987 3.5 97.6
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2ESK AND 2ZFY 3.2987 49.121 1.99 60402 60385 3053 99.54 0.2356 0.2332 0.2371 0.2802 0.2828
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] -4.7794 -2.5662 3.1302 1.6492
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.511 f_angle_d 0.938 f_chiral_restr 0.07 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26568 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MxDC data collection PHASER phasing PHENIX refinement XDS data reduction XDS data scaling