6YQ5 | pdb_00006yq5

Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - NMR Ensemble


ELECTRON MICROSCOPY - SOLID-STATE NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
14D HNhhNH100 % u-2H13C15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
23D HChH100 % isoleucine-(1HD1, 13CD1)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
33D HChH100 % leucine-(1HD, 13CD)proR-valine-(1HG, 13CG)proR-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
42D hCH100 % isoleucine-(1HD1, 13CD1)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
52D hCH100 % alanine-(1HB, 13CB)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
62D hCH100 % leucine-(1HD, 13CD)proR-valine-(1HG, 13CG)proR-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
72D hCH100 % threonine-(1HG2, 13CG2)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
82D hCH100 % methionine-(1HE, 13CE)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
92D hCH100 % alanine-(1HB, 13CB)- isoleucine-(1HD1, 13CD1)-( 1HG2, 13CG2)-leucine-(1HD, 13CD)proR/proS-valine-(1HG, 13CG)proR/proS-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
103D HNhH100 % isoleucine-(1HD1, 13CD1)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
113D HNhH100 % 50% isoleucine-(1HD1, 13CD1)-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
123D HNhH100 % alanine-(1HB, 13CB)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
133D HNhH100 % 50% alanine-(1HB, 13CB)-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
183D HNhH100 % leucine-(1HD, 13CD)proR-valine-(1HG, 13CG)proR-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
173D HNhH100 % 50% leucine-(1HD, 13CD)proR- valine-(1HG, 13CG)proR-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
163D HNhH100 % threonine-(1HG2, 13CG2)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
143D HNhH100 % 50% threonine-(1HG2, 13CG2)-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
153D HNhH100 % methionine-(1HE, 13CE)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTAsolid0.5 M7.41 atm291Bruker AVANCE 900
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE900
NMR Refinement
MethodDetailsSoftware
naInferential Structure Determination (ISD)
NMR Ensemble Information
Conformer Selection Criteriatarget function
Conformers Calculated Total Number500
Conformers Submitted Total Number10
Representative Model1 (target function)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpinBruker Biospin
5processingTopSpinBruker Biospin
4data analysisCcpNmr AnalysisCCPN
6structure calculationInferential Structure Determination (ISD)Rieping, Nilges, Habeck
Sample
helical arrangement of hexameric rings of gp17.1
Specimen Preparation
Sample Aggregation StateHELICAL ARRAY
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles5965
Reported Resolution (Å)4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC6
Axial Rise38.46
Angular Rotation21.89
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)70
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI ARCTICA
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONCTFFIND4
RECONSTRUCTIONRELION2.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION