4V50 | pdb_00004v50

Crystal Structure of Ribosome with messenger RNA and the Anticodon stem-loop of P-site tRNA.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AVY	pdb entries 2AVY, 2AW4, 2AW7, 2AWB
experimental model	PDB	2AW4	pdb entries 2AVY, 2AW4, 2AW7, 2AWB
experimental model	PDB	2AW7	pdb entries 2AVY, 2AW4, 2AW7, 2AWB
experimental model	PDB	2AWB	pdb entries 2AVY, 2AW4, 2AW7, 2AWB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	7.5	277	MPD, PEG 8000, MGCL2, NH4CL, SPERMINE, SPERMIDINE, TRIS, EDTA, pH 7.5, batch, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.783	α = 90
b = 395.223	β = 90
c = 744.383	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		2006-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.116	ALS	12.3.1

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	3.22	70	75.5			997175	753057	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.22	3.26	11.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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 2AVY, 2AW4, 2AW7, 2AWB	3.22	70	2	997175	753057	37290		0.287	0.26	0.32	0.29	Random	105.753

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
c_angle_deg	0.93743
c_bond_d	0.002842

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18538
Nucleic Acid Atoms	33316
Solvent Atoms
Heterogen Atoms	370

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	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.