9ZB9 | pdb_00009zb9

Cryo-EM Structure of Human GGPPS Bound to Selective Inhibitor CML-07-119

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.8625
f_angle_d	0.4392
f_chiral_restr	0.031
f_bond_d	0.0041
f_plane_restr	0.0029

Sample
Human GGPPS bound to Inhibitor CML-07-119

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1582611
Reported Resolution (Å)	1.95
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	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2200
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
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC
MODEL REFINEMENT	PHENIX	2.0_5729
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
RECONSTRUCTION	cryoSPARC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		11731724	Picks obtained using the cryoSPARC Template Picker supplied with 2D classes obtained from the cryoSPARC Blob Picker which was run on 100 of the micrographs