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Structure of the PR-DUB complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 291 0.1 M Bis-Tris propane pH 8.5, 0.05 M potassium iodide, 13% (w/v) PEG 3350 and 10% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 3.24 62.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.17 α = 90 b = 65.63 β = 114.35 c = 162.76 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS EIGER X 16M 2017-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.5 43.672 98.8 0.998 7.1 2.8 18300 112.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.83 99.1 0.613 1.4 2.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4UEM 3.5 43.672 1.37 15404 730 83.11 0.2465 0.2442 0.2468 0.294 0.2962 132.2666
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 2.208 f_angle_d 0.557 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5875 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Coot model building PHASER phasing