8Z81

Photosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5Y5S 
experimental modelPDB 1NKZ 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.738
f_angle_d3.641
f_chiral_restr0.108
f_bond_d0.008
f_plane_restr0.005
Sample
Photosynthetic LH2-LH1 complex from the purple phototrophic bacterium Halorhodospira halophila
Sample Components
LH2-LH1 complex of Halorhodospira halophila
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles126108
Reported Resolution (Å)2.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (5Y5S, 1NKZ)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value70
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1100
Maximum Defocus (nm)2700
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
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY331335