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Ser65 phosphorylated ubiquitin, major conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.92 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.563 α = 96.86 b = 53.285 β = 104.94 c = 56.866 γ = 110.96
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 PILATUS 6M 2014-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.9 32.28 97.3 0.124 4.6 1.8 39104
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 1.9 1.94 96.3 0.425 2.1 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ubq 1.9 32.28 1.99 39071 1904 97.2 0.1956 0.1934 0.1966 0.2375 0.2392 random
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 13.408 f_angle_d 0.997 f_chiral_restr 0.036 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4559 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing