☰ Navigation Tabs
Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Protein solution: 4mg/mL Kl Dcp1/Dcp2/Edc3, 1mM Edc1 peptide, 6mM substrate analog, 10mM magnsium chloride.
Well solution: 0.22M magnesium chloride, 0.03M EDTA, 8% PEG 8000.
Procedure: 250nL protein solution + 250nL well solution + 50nL 1:10000 seed stock. Set up at RT, grow crystals at 4C.
Crystal Properties Matthews coefficient Solvent content 2.96 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.26 α = 90 b = 83.25 β = 93.62 c = 104.3 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 100 PIXEL DECTRIS PILATUS3 S 6M 2017-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
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 2.84 50 98.7 0.058 9.82 2.9 68126
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 2.84 3 99.1 0.78 1.3 2.8
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 5LOP 2.84 45.96 1.36 35286 1998 99.7 0.227 0.225 0.227 0.248 0.2495 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 17.839 f_angle_d 0.721 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8484 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 115
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building