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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3J25
pdb_00003j25
10.2210/pdb3j25/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
TetM*GDPNP bound to 70S E.coli ribosome
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
liquid ethane / Vitrobot Mark IV
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
52701
Reported Resolution (Å)
7.2
Resolution Method
?
Other Details
a modified version of SPIDER program was used for the reconstruction
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation coefficient
Overall B Value
?
Fitting Procedure
?
Details
METHOD--Local refinement, Flexible fitting REFINEMENT PROTOCOL--rigid body
Data Acquisition
Detector Type
TVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å
2
)
20
Imaging Experiment
Date of Experiment
2011-07-01
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
-1000
Maximum Defocus (nm)
-3500
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
75000
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
Coot
?
MODEL FITTING
DireX
?
MODEL FITTING
UCSF Chimera
?
RECONSTRUCTION
SPIDER
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
The volumes were CTF-corrected in defocus groups