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Structure of a pre-translocational E. coli ribosome obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1056
ELECTRON MICROSCOPY
Sample
pre-translocational E. coli ribosome
Sample Components
30S ribosomal protein S2
30S ribosomal subunit protein S3
30S ribosomal subunit protein S4
30S ribosomal subunit protein S5
30S ribosomal subunit protein S6
30S ribosomal subunit protein S7
30S ribosomal subunit protein S8
30S ribosomal subunit protein S9
30S ribosomal subunit protein S10
30S ribosomal subunit protein S11
30S ribosomal subunit protein S12
30S ribosomal subunit protein S13
30S ribosomal subunit protein S14
30S ribosomal subunit protein S15
30S ribosomal subunit protein S16
30S ribosomal subunit protein S17
30S ribosomal subunit protein S18
30S ribosomal subunit protein S19
30S ribosomal subunit protein S20
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
Cryogen Name
ETHANE
Sample Vitrification Details
rapid-freezing in liquid ethane
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
52181
Reported Resolution (Å)
15
Resolution Method
Other Details
WITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RES ...
WITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RESOLUTION OF THE EM MAP.
THE RESOLUTION OF THE ATOMIC MODEL FITTED INTO EMD-1056 (NOMINAL RESOLUTION 15.0 ANGSTROMS) IS THUS ESTIMATED TO BE BETWEEN 2-3 ANGSTROMS. REAL-SPACE REFINEMENT USING RIGID BODIES INTO EM MAP EMD-1056 (FILTERED TO A NOMINAL RESOLUTION OF 15 ANGSTROMS). RIGID BODY DEFINITION: AN AUTONOMOUS SECONDARY STRUCTURE UNIT (E.G. HELIX SEGMENT, HAIRPIN) OF THE
RIBOSOMAL RNA; AN AUTONOMOUS RIBOSOMAL PROTEIN DOMAIN. THE
ATOMIC MODEL USED WAS GENERATED FROM E. COLI MODELS OF X-RAY
CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS.
IN THE ABSENCE OF E. COLI MODELS, STRUCTURES WERE DERIVED DIRECTLY
FROM THE X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER
ORGANISMS.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Minimization of number of poor van der Waals contacts and maximation of
correlation coefficient