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Cryo-EM structure of human DHX9 in complex with ATX-968 and ADP.
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
Data Collection
Overall
ID #
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
Rrim I (All)
Rpim I (All)
CC (Half)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
1
3.4
49.73
100
0.151
0.157
0.042
0.998
11.8
13.6
81625
Highest Resolution Shell
ID #
Resolution (High)
Resolution (Low)
Percent Possible (All)
Percent Possible (Observed)
R Merge I (Observed)
Rrim I (All)
Rpim I (All)
CC (Half)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
1
3.4
3.46
100
3.612
3.747
0.994
0.5
14
Sample
Human DHX9 bound to ATX-968 and ADP.
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Sample was centrifuged at 21,000 x g for 10 minutes at 6 degrees Celsius and diluted to 0.5 mg/mL (4.34 micromolar) just before grid preparation. 3 mi ...
Sample was centrifuged at 21,000 x g for 10 minutes at 6 degrees Celsius and diluted to 0.5 mg/mL (4.34 micromolar) just before grid preparation. 3 microlitres of the sample was applied to the grid, blotted for 3 seconds with a blot force of 3, and immediately flash frozen.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
985972
Reported Resolution (Å)
2.8
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Overall B Value
64.98
Fitting Procedure
Details
Initial fit was done in Chimera, followed by chain adjustments in Coot and refinement in Phenix.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
60
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
400
Maximum Defocus (nm)
1800
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
165000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Preliminary grid screening was performed in a Glacios.