1VVJ | pdb_00001vvj

Crystal Structure of Frameshift Suppressor tRNA SufA6 bound to Codon CCC-G on the Ribosome

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I9D	PDB ENTRY 3I9D AND 3I93
experimental model	PDB	3I93	PDB ENTRY 3I9D AND 3I93

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10mM MgCl, pH 7.0, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.5456	α = 90
b = 449.211	β = 90
c = 619.2374	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	ADSC QUANTUM 315		2010-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.26	34.82	98.1	0.195	6.57		881904	881904	-3	-3	74.1738879887

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.26	3.34	94.7		0.012	1.05

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		PDB ENTRY 3I9D AND 3I93	3.44000111574	34.8114649848	0.855741124575	755367	34668	98.6907294078	0.245027068825	0.24314615884	0.24	0.284522132625	0.28	8.82233247901

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	18.1339458384
f_angle_d	1.21795491551
f_chiral_restr	0.0679249617986
f_plane_restr	0.0079896293099
f_bond_d	0.0065627471557

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	92228
Nucleic Acid Atoms	198206
Solvent Atoms
Heterogen Atoms	689

Software

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