5J4D | pdb_00005j4d

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	3.1 uL 70SmRNAtRNAfMet 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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.