4V4V | pdb_00004v4v

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 StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Detailsrapid-freezing in liquid ethane
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles52181
Reported Resolution (Å)15
Resolution Method
Other DetailsWITH 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 TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetMinimization of number of poor van der Waals contacts and maximation of correlation coefficient
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--CNS implementation of RSRef
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment2002-07-01
Temperature (Kelvin)93
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1.1
Maximum Defocus (nm)3.8
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification50000
Calibrated Magnification49696
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCNS
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
CTF correction of 3D-maps by Wiener filtration