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 |
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
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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 |
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Spectrometer | Manufacturer | Model | Field Strength |
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1 | Bruker | AVANCE II | 600 |
2 | Varian | INOVA | 800 |
NMR Ensemble Information |
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Conformer Selection Criteria | |
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Conformers Calculated Total Number | |
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Conformers Submitted Total Number | 10 |
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Computation: NMR Software |
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# | Classification | Version | Software Name | Author |
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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 |
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tetrahedral amino-peptidase from P. horikoshii |
Specimen Preparation |
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Sample Aggregation State | PARTICLE |
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Vitrification Instrument | FEI VITROBOT MARK IV |
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Cryogen Name | ETHANE |
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Sample Vitrification Details | Blotting time 2s, force 1, drain time 0. |
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3D Reconstruction |
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Reconstruction Method | SINGLE PARTICLE |
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Number of Particles | 27130 |
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Reported Resolution (Å) | 4.1 |
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Resolution Method | FSC 0.143 CUT-OFF |
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Other Details | |
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Refinement Type | |
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Symmetry Type | POINT |
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Point Symmetry | T |
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Map-Model Fitting and Refinement |
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Id | 1 |
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Refinement Space | |
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Refinement Protocol | OTHER |
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Refinement Target | |
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Overall B Value | |
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Fitting Procedure | |
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Details | |
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Data Acquisition |
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Detector Type | GATAN K2 SUMMIT (4k x 4k) |
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Electron Dose (electrons/Å**2) | 40 |
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Imaging Experiment | 1 |
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Date of Experiment | |
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Temperature (Kelvin) | |
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Microscope Model | FEI POLARA 300 |
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Minimum Defocus (nm) | |
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Maximum Defocus (nm) | |
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Minimum Tilt Angle (degrees) | |
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Maximum Tilt Angle (degrees) | |
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Nominal CS | 2 |
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Imaging Mode | BRIGHT FIELD |
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Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
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Nominal Magnification | 20000 |
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Calibrated Magnification | 25773 |
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Source | FIELD EMISSION GUN |
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Acceleration Voltage (kV) | 300 |
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Imaging Details | |
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EM Software |
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Task | Software Package | Version |
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PARTICLE SELECTION | RELION | 1.4 |
IMAGE ACQUISITION | Latitude | 3 |
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CTF CORRECTION | CTFFIND | 3 |
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MODEL FITTING | iMODFIT | 1.44 |
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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 |
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details |
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PHASE FLIPPING AND AMPLITUDE CORRECTION | | 30407 | |