7QTT | pdb_00007qtt

Structural organization of a late activated human spliceosome (Baqr, core region)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FF4
experimental model	PDB	6FF7
experimental model	PDB	5Z57
experimental model	PDB	6QDV

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.038
f_angle_d	0.833
f_chiral_restr	0.05
f_plane_restr	0.007
f_bond_d	0.004

Sample
Late human activated spliceosome arrested with a dominant-negative mutant of the splicing helicase Aquarius (Aquarius K829A)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Volumes of 4 ul of the concentrated sample were applied to one side of glow-discharged UltrAuFoil 200 2/2 grids (Quantifoil) in a Vitrobot Mark IV (FEI) operating at 4 degrees Celsius and 100% humidity. The grids were blotted for 2s with blotting force 5 and immediately frozen by plunging into liquid ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	146157
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6FF4, 6FF7, 5Z57, 6QDV)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value	177.21
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	45.47

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Warp
IMAGE ACQUISITION	EPU
CTF CORRECTION	Warp
MODEL FITTING	Coot	0.9.6
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.19.2_4158

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		734691