9RFW | pdb_00009rfw

Manikomycin bound to the Escherichia coli 50S ribosomal subunit


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it14.406
r_lrange_other14.406
r_dihedral_angle_6_deg13.519
r_dihedral_angle_3_deg12.617
r_scangle_it10.072
r_scangle_other10.072
r_mcangle_it8.111
r_mcangle_other8.11
r_dihedral_angle_2_deg7.325
r_dihedral_angle_1_deg6.947
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it14.406
r_lrange_other14.406
r_dihedral_angle_6_deg13.519
r_dihedral_angle_3_deg12.617
r_scangle_it10.072
r_scangle_other10.072
r_mcangle_it8.111
r_mcangle_other8.11
r_dihedral_angle_2_deg7.325
r_dihedral_angle_1_deg6.947
r_scbond_it6.428
r_scbond_other6.427
r_mcbond_it5.524
r_mcbond_other5.524
r_angle_refined_deg1.119
r_angle_other_deg0.37
r_dihedral_angle_other_2_deg0.353
r_nbtor_refined0.229
r_symmetry_nbd_other0.195
r_nbd_refined0.158
r_xyhbond_nbd_refined0.14
r_symmetry_nbtor_other0.079
r_symmetry_xyhbond_nbd_other0.056
r_chiral_restr0.049
r_gen_planes_refined0.012
r_bond_refined_d0.007
r_gen_planes_other0.001
r_bond_other_d
Sample
Manikomycin bound 50S ribosomal subunit
Specimen Preparation
Sample Aggregation StateCELL
Vitrification Instrument
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles251301
Reported Resolution (Å)2.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)300
Maximum Defocus (nm)1000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION5.0.0
MODEL REFINEMENTREFMAC5.8.0425
RECONSTRUCTIONRELION5.0.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION483608