7O9K | pdb_00007o9k

Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OOL

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.016
r_lrange_it	23.959
r_dihedral_angle_3_deg	16.741
r_dihedral_angle_4_deg	13.819
r_scangle_it	10.203
r_mcangle_it	9.962
r_scbond_it	5.996
r_dihedral_angle_1_deg	5.773
r_mcbond_it	5.681
r_angle_refined_deg	1.033
r_metal_ion_refined	0.429
r_nbtor_refined	0.284
r_nbd_refined	0.166
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.087
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other

Sample
55S subunit assembly intermediate

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	39495
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (5OOL)
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	49.2

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Coot	0.93
INITIAL EULER ASSIGNMENT	cryoSPARC	2.15
FINAL EULER ASSIGNMENT	cryoSPARC	2.15
RECONSTRUCTION	cryoSPARC	2.15
MODEL REFINEMENT	REFMAC	5.8.0267

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