6LZ1

Structure of S.pombe alpha-mannosidase Ams1


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LZ1 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.974
f_angle_d0.7146
f_chiral_restr0.0522
f_bond_d0.0099
f_plane_restr0.0045
Sample
Ams1 tetramer
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsblot for 5 seconds before plunging
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles75460
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1 (6LZ1)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)400
Maximum Defocus (nm)1000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatch0.53
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctf1.06
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTRELION2.1
CLASSIFICATIONRELION2.1
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION