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Crystal structure of S. pombe Dcp1 in complex with the decapping enhancer EDC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QKL PDB entry 2QKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 M NaCl, 100 mM NaCitrate pH 5-6
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.179 α = 90 b = 41.452 β = 90 c = 95.626 γ = 90
Symmetry Space Group P 2 21 21
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 PSI PILATUS 6M 2016-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.04 47.813 99.9 0.11 0.999 17.4 12.7 10434
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 2.04 2.15 99.7 1.21 2.6 12.4
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 PDB entry 2QKL 2.043 47.813 1.34 10391 523 99.86 0.197 0.1957 0.1982 0.2221 0.2242
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 16.838 f_angle_d 0.862 f_chiral_restr 0.058 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1171 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building SCALA data scaling PHASER phasing XDS data reduction