4V9N | pdb_00004v9n

Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F1G	PDB ENTRY 3F1G AND 3F1H
experimental model	PDB	3F1H	PDB ENTRY 3F1G AND 3F1H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 212.07	α = 90
b = 454.4	β = 90
c = 618.45	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				2012-08-02	M	SINGLE WAVELENGTH
2	1	x-ray	100				2012-02-12	M	SINGLE WAVELENGTH
3	1	x-ray	100				2012-02-29	M	SINGLE WAVELENGTH
4	1	x-ray	100				2011-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1
2	SYNCHROTRON	ALS BEAMLINE 12.3.1		ALS	12.3.1
3	SYNCHROTRON	SSRL BEAMLINE BL9-1		SSRL	BL9-1
4	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	3.4	50			7		807927

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3F1G AND 3F1H	3.4	49.672	1.99	807927	16161	99.65	0.235	0.2343	0.24	0.2681	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]
-3.5525			14.5549		-11.0024

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.745
f_angle_d	0.621
f_chiral_restr	0.053
f_bond_d	0.004
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21929
Nucleic Acid Atoms	34186
Solvent Atoms
Heterogen Atoms	1285

Software

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