4V63 | pdb_00004v63

Structural basis for translation termination on the 70S ribosome.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J00	PROTEIN DATA BANK ACCESSION CODES 2J00,2J01,2J02 AND 2J03.
experimental model	PDB	2J01	PROTEIN DATA BANK ACCESSION CODES 2J00,2J01,2J02 AND 2J03.
experimental model	PDB	2J02	PROTEIN DATA BANK ACCESSION CODES 2J00,2J01,2J02 AND 2J03.
experimental model	PDB	2J03	PROTEIN DATA BANK ACCESSION CODES 2J00,2J01,2J02 AND 2J03.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	296	100 mM TRIS-OAc, 200 mM KSCN, 3.5-4.5 % (w/v) PEG20K, 4-9 % PEG200, DEOXY BIGCHAP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.13	α = 90
b = 454.39	β = 90
c = 616.45	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	CCD	MARMOSAIC 300 mm CCD	Si(111) Double Crystal Monochromator. Adjustable focusing mirrors in K-B geometry	2007-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.95370	APS	23-ID-D

Data Collection

Overall
ID #	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
1	3.2	50	95.9	0.271	0.271	8.21	12.4		906561			53.87

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.3	89		0.795	0.795	2.85	7

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)	Mean Isotropic B
X-RAY DIFFRACTION		PROTEIN DATA BANK ACCESSION CODES 2J00,2J01,2J02 AND 2J03.	3.207	49.901	2.03	906561	8284	95.14	0.292	0.292	0.29	0.319	0.32	153.726

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]
-36.555			-30.132		-27.284

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.797
f_angle_d	0.708
f_chiral_restr	0.031
f_bond_d	0.003
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	96544
Nucleic Acid Atoms	200836
Solvent Atoms
Heterogen Atoms	2581

Software

Software
Software Name	Purpose
PHENIX	refinement
CNS	refinement
XDS	data reduction
XDS	data scaling
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.