6NBC

human methemoglobin state 1 determined using single-particle cryo-EM at 200 keV


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4N7P 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.095
f_angle_d1.003
f_chiral_restr0.055
f_plane_restr0.011
f_bond_d0.009
Sample
methemoglobin from human
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsSample was manually blotted for 4-5 seconds using Whatman No. 1 filter paper immediately prior to plunge-freezing.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles24308
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (4N7P)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value67
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)69
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)5000
Maximum Defocus (nm)16000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification73000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION2.1
IMAGE ACQUISITIONLeginon3.2
CTF CORRECTIONCTFFIND4
MODEL FITTINGUCSF Chimera1.11.2
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTRELION2.1
CLASSIFICATIONRELION2.1
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.11.1_2580
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1232543Difference-of-Gaussian-picked.