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Crystal structure of depupylase Dop in complex with Pup and ADP/trifluoromagnesate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LRT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 100 mM Tris-acetate pH 7.0-8.5, 10 mM ADP, 40 mM MgCl2, 16 mM NaF, 4 mM BeSO4 and 0.75-1.0 M KH2PO4
Crystal Properties Matthews coefficient Solvent content 2.9 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.334 α = 90 b = 106.334 β = 90 c = 107.384 γ = 120
Symmetry Space Group P 31 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 2020-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.88 47.65 100 0.131 0.134 0.03 0.999 15.5 20.2 57471 29.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.92 100 1.72 1.765 0.396 0.785 19.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5LRT 1.88 47.65 1.34 57429 2960 99.98 0.1605 0.159 0.1579 0.188 0.1855 33.8445
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3986 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction