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Cryo-EM structure of Sr01-080, a denovo designed borneol dehydrogenase
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
12.85
f_angle_d
0.5185
f_chiral_restr
0.0428
f_plane_restr
0.0088
f_bond_d
0.0026
Sample
01_80
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
743562
Reported Resolution (Å)
3.17
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Non-uniform refinement in CryosPARC with D2 symmetry and refinement mask excluding neighboring particles in psuedo-filaments present in micrographs.
Refinement Type
Symmetry Type
POINT
Point Symmetry
D2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Initial fitting was done in chimeraX, and refined through sequential Real space refinement protocol in PHENIX and manual refinement with ISOLDE
Data Acquisition
Detector Type
FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)
52.88
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS GLACIOS
Minimum Defocus (nm)
600
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
100000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
MODEL REFINEMENT
PHENIX
2.0_5824
RECONSTRUCTION
cryoSPARC
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
3922227
Particles were picked using Blob Picker in CryoSPARC with min particle diameter 80 A, max particle diameter 120 A, and min separation distance 40 A. 5974094 picks were reduced with an Inspect Picks Job to 4494189, and an Extract Mics. (G) job reduced picks further to 3922227.