☰ Navigation Tabs
Structure of K11-linked di-ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ PDB ENTRY 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 292 25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.03 39.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.597 α = 90 b = 56.059 β = 95.21 c = 65.772 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 298 CCD ADSC QUANTUM 315 MIRRORS 2010-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 2.19 30 99.9 0.057 18.7 3.7 29153 -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) 1 2.19 2.28 99.9 0.46 3 3.6
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 1UBQ 2.19 29.23 1.34 29153 29142 1481 99.3 0.247 0.245 0.2435 0.281 0.2789
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] -6.2024 -0.0421 3.2976 2.9048
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.527 f_angle_d 0.932 f_chiral_restr 0.049 f_bond_d 0.008 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4806 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 35
Software Software Software Name Purpose BOS data collection PHASER phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling