9FY2 | pdb_00009fy2

Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.086
r_long_range_B_refined	13.183
r_long_range_B_other	13.183
r_scangle_other	9.418
r_mcangle_it	9.04
r_mcangle_other	9.04
r_dihedral_angle_2_deg	8.643
r_dihedral_angle_1_deg	7.569
r_scbond_it	6.011
r_scbond_other	6.011
r_mcbond_it	5.791
r_mcbond_other	5.79
r_angle_refined_deg	1.541
r_angle_other_deg	0.576
r_chiral_restr	0.064
r_gen_planes_refined	0.011
r_bond_refined_d	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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
Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site
Sample Components
Bacillus subtilis 70S ribosome
Nascent Chain CliM
mRNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	368433
Reported Resolution (Å)	2.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	1.14

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	300
Maximum Defocus (nm)	900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0415

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION