5OGW | pdb_00005ogw

Cryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.842
r_long_range_B_refined20.053
r_long_range_B_other20.053
r_scangle_other13.4
r_mcangle_it10.792
r_mcangle_other10.791
r_dihedral_angle_4_deg9.302
r_dihedral_angle_3_deg8.416
r_scbond_it7.932
r_scbond_other7.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.842
r_long_range_B_refined20.053
r_long_range_B_other20.053
r_scangle_other13.4
r_mcangle_it10.792
r_mcangle_other10.791
r_dihedral_angle_4_deg9.302
r_dihedral_angle_3_deg8.416
r_scbond_it7.932
r_scbond_other7.932
r_dihedral_angle_1_deg6.648
r_mcbond_it6.523
r_mcbond_other6.523
r_angle_refined_deg1.374
r_angle_other_deg1.129
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Plasmodium falciparum actin 1 filament stabilized by jasplakinolide
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentGATAN CRYOPLUNGE 3
Cryogen NameETHANE
Sample Vitrification DetailsSample (2 uL of JAS-stabilized F-actin solution) was applied to a glow-discharged holey carbon grid, incubated for 30 s and manually blotted for 4 s f ...Sample (2 uL of JAS-stabilized F-actin solution) was applied to a glow-discharged holey carbon grid, incubated for 30 s and manually blotted for 4 s from the backside with filter paper.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles140716
Reported Resolution (Å)3.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)110
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsCs corrected microscope
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONSPARXv3.0
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.0.7
CTF CORRECTIONRELION1.4
MODEL FITTINGMODELLER
MODEL FITTINGUCSF Chimera
MODEL FITTINGiMODFIT
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
RECONSTRUCTIONRELION1.4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION144058