5UMD | pdb_00005umd

Structure of the Plasmodium falciparum 80S ribosome bound to the antimalarial drug mefloquine


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.186
r_dihedral_angle_1_deg24.185
r_dihedral_angle_3_deg17.842
r_dihedral_angle_4_deg11.957
r_long_range_B_refined7.98
r_mcangle_it2.496
r_mcbond_it1.344
r_scbond_it1.19
r_angle_refined_deg0.875
r_chiral_restr0.339
Sample
Plasmodium falciparum 80S ribosome bound to mefloquine
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles43184
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value129.3
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification78000
Calibrated Magnification104748
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONRELION1.3
CTF CORRECTIONCTFFIND3
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION1.3
FINAL EULER ASSIGNMENTRELION1.3
CLASSIFICATIONRELION1.3
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTREFMAC5.8
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION