8GFT | pdb_00008gft

Hsp90 provides platform for CRaf dephosphorylation by PP5

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FWL
experimental model	PDB	1WAO
experimental model	PDB	1S95

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.952
f_angle_d	0.581
f_chiral_restr	0.05
f_bond_d	0.006
f_plane_restr	0.004

Sample
Hsp90:Cdc37:CRaf:PP5 complex
Sample Components
Protein Phosphatase 5 (H304A)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details	3uL OF SAMPLE, 10C, 100% HUMIDITY, 30S WAIT TIME, 3S BLOT TIME, -2 BLOT FORCE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	545237
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain: 43k p ...	Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain: 43k particles, 3.8A Composite half maps were used to get the final resolution in Relion PostProcessing. All original maps provided in the "Related entries" tab.
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (5FWL, 1WAO, 1S95)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	This model was built using rigid body docking in Chimera and ChimeraX for all main chains, and RosettaCM to add remaining fragments not included in pr ...	This model was built using rigid body docking in Chimera and ChimeraX for all main chains, and RosettaCM to add remaining fragments not included in previous models. Refinement was done using iterative Phenix and RosettaRelax, and finalized with ISOLDE.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	69

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.3.2
IMAGE ACQUISITION	SerialEM	3.8-beta
CTF CORRECTION	RELION	3.1.3
MODEL FITTING	ISOLDE	1.0b3
MODEL FITTING	UCSF Chimera	1.15
MODEL FITTING	UCSF ChimeraX	1.2.5
MODEL FITTING	Rosetta	3.11
MODEL FITTING	PHENIX	1.20.1-4487
MODEL REFINEMENT	PHENIX	1.20.1-4487
INITIAL EULER ASSIGNMENT	RELION	3.1.3
FINAL EULER ASSIGNMENT	RELION	3.1.3
CLASSIFICATION	RELION	3.1.3
RECONSTRUCTION	RELION	3.1.3
RECONSTRUCTION	UCSF ChimeraX	1.2.5

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3730385	Gaussian blob particle picking in cryosparc.

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.