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Structure of an active ligase (HOIP)/ubiquitin transfer complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LJQ pdb entry 4LJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.1 M carboxylic acids, 0.1 M imidazole, MES, 30 % P550 MME_P20K, pH 6.5, vapour diffusion, temperature 293K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.46 50.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.95 α = 90 b = 45.95 β = 90 c = 133.01 γ = 120
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 2012-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.920 Diamond I02
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 1.56 44.34 99.2 0.039 12.2 3.4 88818 44055 -3 27.559
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 1.56 1.6 94 0.593 1.52
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 4LJQ 1.564 44.337 0.73 44055 2220 94.6 0.1828 0.1812 0.1867 0.2124 0.2154 39.0035
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 13.877 f_angle_d 1.032 f_chiral_restr 0.071 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CCP4 refinement XSCALE data scaling CCP4 data reduction CCP4 data scaling