9S2U | pdb_00009s2u

1:1 complex of M.tuberculosis MmpL5 and M.smegmatis AcpM

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	40.608
r_long_range_B_other	40.608
r_mcangle_it	23.867
r_mcangle_other	23.864
r_scangle_other	23.64
r_dihedral_angle_3_deg	15.825
r_mcbond_it	14.596
r_mcbond_other	14.595
r_scbond_it	13.506
r_scbond_other	13.504
r_dihedral_angle_1_deg	4.449
r_dihedral_angle_2_deg	2.024
r_angle_refined_deg	1.234
r_angle_other_deg	0.427
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.001
r_bond_other_d
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
1:1 complex of M.tuberculosis MmpL5 and M.smegmatis AcpM

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	78900
Reported Resolution (Å)	3.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

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

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	80

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	2200
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.6.2
IMAGE ACQUISITION	EPU
MODEL FITTING	UCSF ChimeraX	1.8
INITIAL EULER ASSIGNMENT	cryoSPARC	4.6.2
FINAL EULER ASSIGNMENT	cryoSPARC	4.6.2
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		4185525