8BGW
CryoEM structure of quinol-dependent Nitric Oxide Reductase (qNOR) from Alcaligenes xylosoxidans at 2.2 A resolution
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.71 |
r_dihedral_angle_3_deg | 16.396 |
r_dihedral_angle_4_deg | 16.157 |
r_lrange_it | 13.388 |
r_lrange_other | 13.388 |
r_scangle_it | 9.63 |
r_scangle_other | 9.629 |
r_mcangle_it | 8.426 |
r_mcangle_other | 8.425 |
r_dihedral_angle_1_deg | 6.941 |
Sample |
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quinol-dependent Nitric Oxide Reductase |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Sample at 3 mg/mL was applied to glow-discharged Quantifoil Au R1.2/1.3 holey carbo grids |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 404950 |
Reported Resolution (Å) | 2.2 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | 47 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 34.9 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 900 |
Maximum Defocus (nm) | 2700 |
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 | 130000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | 1.6.1 |
IMAGE ACQUISITION | EPU | 2.14 |
CTF CORRECTION | CTFFIND | 4.1 |
MODEL FITTING | MOLREP | 11.06.04 |
MODEL REFINEMENT | REFMAC | 5.8.0267 |
MODEL REFINEMENT | PHENIX | 1.2 |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 3000000 |