5J4D

E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details 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 Data

Unit Cell
Length (Å) Angle (°)
a = 211.54 α = 90
b = 454.4 β = 90
c = 619.47 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
3 100
4 100
5 100
6 100
7 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2015-07-26
PIXEL DECTRIS PILATUS3 6M -- 2015-07-01
PIXEL DECTRIS PILATUS3 6M -- 2015-07-01
PIXEL DECTRIS PILATUS 6M -- 2015-07-26
PIXEL DECTRIS PILATUS 6M -- 2015-07-26
PIXEL DECTRIS PILATUS3 6M -- 2015-07-01
PIXEL DECTRIS PILATUS 6M -- 2015-07-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
3.1 70 100.0 -- -- -- 37.4 -- 1174254 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
-- -- -- -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.1 49.977 -- 1.35 -- 1064934 21298 99.81 -- 0.2221 0.2214 0.2563 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.1 3.1352 -- 707 34661 0.361 0.3784 -- 100.0
X Ray Diffraction 3.1352 3.1721 -- 707 34600 0.3484 0.3715 -- 100.0
X Ray Diffraction 3.1721 3.2108 -- 706 34669 0.3405 0.3771 -- 100.0
X Ray Diffraction 3.2108 3.2514 -- 708 34654 0.3293 0.3548 -- 100.0
X Ray Diffraction 3.2514 3.2942 -- 706 34605 0.3204 0.3449 -- 100.0
X Ray Diffraction 3.2942 3.3393 -- 707 34655 0.3102 0.3533 -- 100.0
X Ray Diffraction 3.3393 3.387 -- 707 34651 0.3025 0.3354 -- 100.0
X Ray Diffraction 3.387 3.4375 -- 708 34681 0.2919 0.3173 -- 100.0
X Ray Diffraction 3.4375 3.4912 -- 707 34663 0.2869 0.3268 -- 100.0
X Ray Diffraction 3.4912 3.5485 -- 709 34738 0.2817 0.3266 -- 100.0
X Ray Diffraction 3.5485 3.6096 -- 707 34647 0.276 0.3183 -- 100.0
X Ray Diffraction 3.6096 3.6753 -- 709 34728 0.2574 0.3029 -- 100.0
X Ray Diffraction 3.6753 3.7459 -- 709 34743 0.2478 0.2964 -- 100.0
X Ray Diffraction 3.7459 3.8224 -- 709 34739 0.2355 0.2697 -- 100.0
X Ray Diffraction 3.8224 3.9054 -- 709 34717 0.225 0.2637 -- 100.0
X Ray Diffraction 3.9054 3.9963 -- 709 34763 0.2182 0.2562 -- 100.0
X Ray Diffraction 3.9963 4.0961 -- 709 34737 0.2152 0.2523 -- 100.0
X Ray Diffraction 4.0961 4.2068 -- 710 34785 0.2087 0.244 -- 100.0
X Ray Diffraction 4.2068 4.3306 -- 711 34849 0.2009 0.2384 -- 100.0
X Ray Diffraction 4.3306 4.4703 -- 710 34776 0.2009 0.2463 -- 100.0
X Ray Diffraction 4.4703 4.6299 -- 711 34831 0.1906 0.2201 -- 100.0
X Ray Diffraction 4.6299 4.8152 -- 712 34924 0.1899 0.2362 -- 100.0
X Ray Diffraction 4.8152 5.0341 -- 713 34898 0.1847 0.2272 -- 100.0
X Ray Diffraction 5.0341 5.2992 -- 712 34901 0.1734 0.2152 -- 100.0
X Ray Diffraction 5.2992 5.6308 -- 713 34954 0.1676 0.212 -- 100.0
X Ray Diffraction 5.6308 6.0649 -- 714 35012 0.1748 0.2227 -- 100.0
X Ray Diffraction 6.0649 6.674 -- 717 35124 0.1832 0.225 -- 100.0
X Ray Diffraction 6.674 7.6368 -- 718 35191 0.1796 0.2108 -- 100.0
X Ray Diffraction 7.6368 9.6103 -- 723 35444 0.1928 0.211 -- 100.0
X Ray Diffraction 9.6103 49.9833 -- 701 34296 0.2071 0.2183 -- 95.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.072
f_dihedral_angle_d 18.944
f_bond_d 0.007
f_chiral_restr 0.045
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 97108
Nucleic Acid Atoms 201010
Heterogen Atoms 2903
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
XDS data reduction
XSCALE data scaling
PHENIX phasing
Blu-Ice data collection