6RVD | pdb_00006rvd

Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6E1H
experimental model	PDB	6RTW
experimental model	PDB	6RVC

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.47
f_angle_d	1.166
f_chiral_restr	0.064
f_bond_d	0.009
f_plane_restr	0.007

Sample
2:1 PTCH1:SHH complex

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	77712
Reported Resolution (Å)	3.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (6E1H, 6RTW, 6RVC)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details	This is a re-refinement of pdb entry 6E1H, also using the high-resolution crystal structures of the isolated PTCH1-ECD1 (pdb 6RTW) and PTCH1-ECD2 (pdb 6RVC).

Data Acquisition
Detector Type	GATAN K2 BASE (4k x 4k)
Electron Dose (electrons/Å**2)	1.6

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

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION
CTF CORRECTION	CTFFIND
MODEL FITTING	Coot	0.9.9.1
MODEL REFINEMENT	PHENIX	1.14

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE