9HDD | pdb_00009hdd

Sla2 C-terminal region (Residues 560-968) (REND and THATCH domains)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P33338-F1

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	74.709
r_long_range_B_other	74.708
r_mcangle_it	51.26
r_mcangle_other	51.255
r_scangle_other	49.306
r_mcbond_it	34.128
r_mcbond_other	34.128
r_scbond_other	31.001
r_scbond_it	31
r_dihedral_angle_3_deg	13.603
r_dihedral_angle_1_deg	8.046
r_dihedral_angle_2_deg	3.292
r_angle_refined_deg	1.847
r_angle_other_deg	0.621
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
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
ScSla2 residues 351-968

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	249299
Reported Resolution (Å)	3.62
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

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

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	45

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2000
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	120000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	ISOLDE
MODEL FITTING	UCSF ChimeraX
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	cryoSPARC	4
FINAL EULER ASSIGNMENT	cryoSPARC	4
CLASSIFICATION	cryoSPARC	4
RECONSTRUCTION	cryoSPARC	4

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