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Serial electron diffraction (SerialED) structure of Y122F mutant Ribonucleotide reductase R2 from E. coli in its oxidised (met) form (re-oxidised)
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 73.95
α = 90
b = 76.54
β = 90
c = 145.74
γ = 90
Symmetry
Space Group
P 21 21 21
Data Collection
Refinement
Statistics
Diffraction ID
Structure Solution Method
Cross Validation method
Resolution (High)
Resolution (Low)
Cut-off Sigma (F)
Number Reflections (Observed)
Number Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (Observed)
R-Work (Depositor)
R-Work (DCC)
R-Free (Depositor)
R-Free (DCC)
Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY
FREE R-VALUE
2
19.93
1.33
49839
1198
88.1
0.2476
0.2467
0.2404
0.2848
0.2679
34.33
Temperature Factor Modeling
Anisotropic B[1][1]
Anisotropic B[1][2]
Anisotropic B[1][3]
Anisotropic B[2][2]
Anisotropic B[2][3]
Anisotropic B[3][3]
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
3.7923
f_angle_d
0.426
f_chiral_restr
0.0337
f_plane_restr
0.0034
f_bond_d
0.0018
Sample
Y122F mutant of Ribonucleotide reductase R2 from E. coli in its oxidised (met) form (re-oxidized)
Specimen Preparation
Sample Aggregation State
3D ARRAY
Vitrification Instrument
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
2
Resolution Method
DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type
3D CRYSTAL
Space Group Name
Length a
73.95
Length b
76.54
Length c
76.54
Angle Alpha
90
Angle Beta
90
Angle Gamma
90
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
OTHER
Refinement Target
Maximum-likelihood
Overall B Value
33.44
Fitting Procedure
Details
Data Acquisition
Detector Type
OTHER
Electron Dose (electrons/Å**2)
1.38
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
1
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
DIFFRACTION
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
To address the preferred orientation of ribbon-shaped crystals on the grid, SerialED data was collected at tilt angles of 0, 10, 25, 45, and 60 degrees. Lower tilts minimized absorption for improved resolution, while higher tilts expanded reciprocal space coverage.