STRUCTURE DETERMINATION OF THE TETRAHEDRAL AMINOPEPTIDASE TET2 FROM P. HORIKOSHII BY USE OF COMBINED SOLID-STATE NMR, SOLUTION-STATE NMR AND EM DATA 4.1 A, FOLLOWED BY REAL_SPACE_REFINEMENT AT 4.1 A
ELECTRON MICROSCOPY - SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
RFDR 3D
20 mM TRIS, 50 mM non sodium chloride
100 % H2O
50 mM
7.5
1 atm
300
Bruker AVANCE II 600
2
DARR
20 mM Tris, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Bruker AVANCE II 600
3
3D 1H-13C NOESY aliphatic
50 mM Tris, 50 mM NaCl
100% D2O
50 mM
8
1 atm
328
Varian INOVA 800
4
CCdream (CC)
20 mM Tris, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Varian INOVA 800
5
NCO
20 mM Tris, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Varian INOVA 800
6
NCOCX
20 mM Tris, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Varian INOVA 800
7
NCACX
20 mM Tris, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Varian INOVA 800
8
CONCACB
20 mM Tris, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Varian INOVA 800
9
CANCOCX
20 mM Tris, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Varian INOVA 800
10
hCANH
20 mM TRIS, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Bruker AVANCE II 600
11
hCONH
20 mM TRIS, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Varian INOVA 600
12
hcoCAcoNH
20 mM TRIS, 50 mM NaCl
100% H2O
50 mM
7.5
1 atm
300
Bruker AVANCE II 600
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
2
Bruker
AVANCE II
600
3
Varian
INOVA
800
4
Varian
INOVA
600
NMR Refinement
Method
Details
Software
simulated annealing
Xplor-NIH
NMR Ensemble Information
Conformer Selection Criteria
structures with the lowest energy
Conformers Calculated Total Number
100
Conformers Submitted Total Number
1
Representative Model
1 (lowest energy)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
collection
TopSpin
3.2
Bruker Biospin
5
collection
VnmrJ
Agilent
2
structure calculation
CYANA
3.97
Guntert, Mumenthaler and Wuthrich
6
chemical shift assignment
CcpNmr Analysis
CCPN
4
peak picking
CcpNmr Analysis
CCPN
7
structure calculation
Xplor-NIH
2.44.8
G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra
Sample
TETRAHEDRAL AMINOPEPTIDASE TET2
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Blotting time 2s, force 1, drain time 0.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
27130
Reported Resolution (Å)
4.1
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
T
Map-Model Fitting and Refinement
Id
1
Refinement Space
Refinement Protocol
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
40
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER