7BL1 | pdb_00007bl1

human complex II-BATS bound to membrane-attached Rab5a-GTP

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DFZ
experimental model	PDB	3MJH
experimental model	PDB	4DDP
experimental model	PDB	3IHY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	264.032
r_mcangle_it	136.303
r_scangle_it	135.451
r_scbond_it	86.101
r_mcbond_it	78.101
r_dihedral_angle_2_deg	33.74
r_dihedral_angle_4_deg	17.49
r_dihedral_angle_3_deg	16.618
r_dihedral_angle_1_deg	9.059
r_angle_refined_deg	1.977

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	264.032
r_mcangle_it	136.303
r_scangle_it	135.451
r_scbond_it	86.101
r_mcbond_it	78.101
r_dihedral_angle_2_deg	33.74
r_dihedral_angle_4_deg	17.49
r_dihedral_angle_3_deg	16.618
r_dihedral_angle_1_deg	9.059
r_angle_refined_deg	1.977
r_nbtor_refined	0.266
r_nbd_refined	0.236
r_chiral_restr	0.126
r_xyhbond_nbd_refined	0.081
r_gen_planes_refined	0.01
r_bond_refined_d	0.007
r_ext_dist_refined_d	0.003

Sample
human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a
Sample Components
human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG)
Ras-related protein Rab-5A

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	Blot force 20, blot time 6 s

3D Reconstruction
Reconstruction Method	SUBTOMOGRAM AVERAGING
Number of Particles	26979
Reported Resolution (Å)	9.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5DFZ, 3MJH, 4DDP, 3IHY)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	correlation
Overall B Value	320
Fitting Procedure
Details	An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. ...	An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with self-restraints (4.3) and restraints to 3MJH, 4DDP and 3IHY.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	2.99

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2000
Maximum Defocus (nm)	5000
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
VOLUME SELECTION	MATLAB	R2016b
IMAGE ACQUISITION	SerialEM	3.8
CTF CORRECTION	NOVACTF	1.0.0
MODEL FITTING	Coot	0.9
MODEL FITTING	ISOLDE	1.1
FINAL EULER ASSIGNMENT	MATLAB	R2016b
CLASSIFICATION	MATLAB	R2016b
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	REFMAC	5.8.0272
MODEL REFINEMENT	ISOLDE	1.1

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.