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Structure of the N-terminal mIF4G domain from S. cerevisiae Upf2, a protein involved in the degradation of mRNAs containing premature stop codons
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 100mM Tris-HCl pH 8.5 and 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 291K 2 VAPOR DIFFUSION, SITTING DROP 9 291 100mM NaCl, 100 mM Bicine pH9 and 30% PEG MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.813 α = 90 b = 50.927 β = 99.96 c = 71.993 γ = 90
Symmetry Space Group P 1 21 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 PSI PILATUS 6M 2012-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9791 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.64 50 98.4 0.052 14.6 3 36645 36059
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.74 95.9 0.626 2.3 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING THROUGHOUT 1.641 41.183 2.01 36645 36056 1803 98.47 0.23 0.1929 0.1909 0.2297 0.2265 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] -4.6915 -1.2267 8.8125 -4.1211
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.984 f_angle_d 0.993 f_chiral_restr 0.071 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2544 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 1
Software Software Software Name Purpose Arcimboldo phasing PHENIX refinement XDS data reduction XSCALE data scaling