9AVI | pdb_00009avi

TolQ inner membrane protein from Acinetobacter baumannii

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	32.442
r_long_range_B_other	32.442
r_scangle_other	23.109
r_dihedral_angle_2_deg	21.889
r_mcangle_it	16.895
r_mcangle_other	16.888
r_dihedral_angle_3_deg	16.506
r_scbond_it	13.603
r_scbond_other	13.595
r_mcbond_it	11.053
r_mcbond_other	11.044
r_dihedral_angle_4_deg	9.465
r_dihedral_angle_1_deg	6.46
r_angle_refined_deg	1.447
r_angle_other_deg	1.333
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d
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
TolQ inner membrane protein

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	215170
Reported Resolution (Å)	3.02
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Map was post processed using DeepEMHancer to guide refinement. The deposited maps are pre-DeepEMHancer
Refinement Type
Symmetry Type	POINT
Point Symmetry	C5

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 (6k x 4k)
Electron Dose (electrons/Å**2)	100

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
RECONSTRUCTION	cryoSPARC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch motion and patch CTF correction with binning to 0.833 A/pixel.	472724	Manual picking to generate templates. Template based autopicking to get 472724 particles. Iterative 2D classification to get 246741 particles.