4V7P | pdb_00004v7p

Recognition of the amber stop codon by release factor RF1.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F1E	PDB ENTRIES 3F1E and 3F1F
experimental model	PDB	3F1F	PDB ENTRIES 3F1E and 3F1F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295.5	crystals were grown by the sitting-drop vapor diffusion method dispensed robotically using 1-2 uL ribosome complexes mixed with 1-2 uL reservoir solution (100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 3.4-4.8% PEG20,000, 2.5-11.5% PEG200) at 22.5 C, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

Crystal Properties
Matthews coefficient	Solvent content
3.339	61.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.38	α = 90
b = 452.7	β = 90
c = 617.09	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					2009-08-05	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D
2	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

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	3.514	89	100			724157	723953		1.1

Refinement

Statistics
Diffraction ID	Structure Solution 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRIES 3F1E and 3F1F	3.62	49.953	1.99	663328	13271	99.99	0.26	0.26	0.25	0.291	0.29	2% 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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.407
f_angle_d	0.659
f_chiral_restr	0.041
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21924
Nucleic Acid Atoms	34121
Solvent Atoms
Heterogen Atoms	2

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CNS	refinement
XDS	data reduction
CNS	phasing

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.