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E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 3.1 uL 70S*mRNA*tRNAfMet complex + 3.1 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate), reservoir: 300 uL 0.5-0.7 M sodium chloride, 4-fold molar excess of E. coli release factor 1 added during complex formation
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.541 α = 90 b = 454.397 β = 90 c = 619.473 γ = 90
Symmetry Space Group P 21 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 DECTRIS PILATUS 6M 2015-07-26 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-07-26 M SINGLE WAVELENGTH 3 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-07-26 M SINGLE WAVELENGTH 4 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-07-26 M SINGLE WAVELENGTH 5 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-07-01 M SINGLE WAVELENGTH 6 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-07-01 M SINGLE WAVELENGTH 7 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2 2 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2 3 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2 4 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2 5 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D 6 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D 7 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.1 70 100 8.28 37.4 1174254
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.1 49.977 1.35 1064934 21298 99.81 0.2221 0.2214 0.2322 0.2563 0.2623
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 18.944 f_angle_d 1.072 f_chiral_restr 0.045 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 97108 Nucleic Acid Atoms 201010 Solvent Atoms Heterogen Atoms 2903
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing Blu-Ice data collection