6F3K | pdb_00006f3k

Combined solid-state NMR, solution-state NMR and EM data for structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii

ELECTRON MICROSCOPY - SOLUTION NMR - SOLID-STATE NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	RFDR 3D	20 mM TRIS, 50 mM 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 sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Varian INOVA 800
5	NCO	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Varian INOVA 800
6	NCOCX	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Varian INOVA 800
7	NCACX	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Varian INOVA 800
8	CONCACB	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Varian INOVA 800
9	CANCOCX	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Varian INOVA 800
10	hCANH	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Bruker AVANCE II 600
11	hCONH	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Bruker AVANCE II 600
12	hcoCAcoNH	20 mM TRIS, 50 mM sodium chloride	100% H2O	50 mM	7.5	1 atm	300	Bruker AVANCE II 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE II	600
2	Varian	INOVA	800

NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number	10

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CcpNmr Analysis		CCPN
2	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
3	chemical shift assignment	CcpNmr Analysis		CCPN
4	peak picking	CcpNmr Analysis		CCPN
5	structure calculation	Xplor-NIH		Schwieters, Kuszewski, Tjandra and Clore

Sample
tetrahedral amino-peptidase from P. horikoshii

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
Nominal Magnification	20000
Calibrated Magnification	25773
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	1.4
IMAGE ACQUISITION	Latitude	3
CTF CORRECTION	CTFFIND	3
MODEL FITTING	iMODFIT	1.44
INITIAL EULER ASSIGNMENT	RELION	1.4
FINAL EULER ASSIGNMENT	RELION	1.4
CLASSIFICATION	RELION	1.4
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	X-PLOR	4.39

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		30407

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.