6QNQ | pdb_00006qnq

70S ribosome initiation complex (IC) with experimentally assigned potassium ions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V6G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	Tris-OAc, KSCN, PEG-20K, PEG-550mme

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.46	α = 90
b = 452.18	β = 90
c = 626.12	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	PSI PILATUS 6M		2008-11-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 12M		2017-12-13	M	SINGLE WAVELENGTH
3	1	x-ray	100	PIXEL	DECTRIS PILATUS 12M		2017-12-13	M	SINGLE WAVELENGTH
4	1	x-ray	100	PIXEL	DECTRIS PILATUS 12M		2017-12-13	M	SINGLE WAVELENGTH
5	1	x-ray	100	PIXEL	DECTRIS PILATUS 12M		2017-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA
2	SYNCHROTRON	DIAMOND BEAMLINE I23	3.351	Diamond	I23
3	SYNCHROTRON	DIAMOND BEAMLINE I23	3.542	Diamond	I23
4	SYNCHROTRON	DIAMOND BEAMLINE I23	3.531	Diamond	I23
5	SYNCHROTRON	DIAMOND BEAMLINE I23	3.542	Diamond	I23

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	3.5	226.09	96.7	0.285	0.177	7.13	12.36		719306			97.49

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	3.5	3.6	88.9		0.568	0.568	1.98	12.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	MOLECULAR REPLACEMENT	THROUGHOUT	4v6g	3.5	226.09	1.99	743746	22128	99.98	0.1893	0.1874	0.2	0.2513	0.25	96.6244

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	94097
Nucleic Acid Atoms	202857
Solvent Atoms
Heterogen Atoms	3553

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.