6QRZ
Crystal structure of R2-like ligand-binding oxidase from Sulfolobus acidocaldarius solved by 3D micro-crystal electron diffraction
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3EE4 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.31 | α = 90 |
b = 108.93 | β = 90 |
c = 48.17 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | Mean Isotropic B | |||||||
ELECTRON CRYSTALLOGRAPHY | FREE R-VALUE | 3 | 28.995 | 1.35 | 4423 | 233 | 62.52 | 0.3189 | 0.3179 | 0.3347 |
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 | 6.546 |
f_angle_d | 0.411 |
f_chiral_restr | 0.035 |
f_plane_restr | 0.003 |
f_bond_d | 0.002 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
Coot | model building |
Sample |
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R2-like ligand-binding oxidase |
Specimen Preparation | |
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Sample Aggregation State | 3D ARRAY |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | CRYSTALLOGRAPHY |
Number of Particles | |
Reported Resolution (Å) | 3 |
Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
Other Details | |
Refinement Type | |
Symmetry Type | 3D CRYSTAL |
Space Group Name | |
Length a | 63.305 |
Length b | 108.925 |
Length c | 108.925 |
Angle Alpha | 90 |
Angle Beta | 90 |
Angle Gamma | 90 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (3EE4) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | OTHER | ||||||||
Electron Dose (electrons/Å**2) | 0.16 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | JEOL 2100 |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | DIFFRACTION |
Specimen Holder Model | GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER |
Nominal Magnification | |
Calibrated Magnification | |
Source | LAB6 |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
MODEL FITTING | Coot | |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE |