EMD-4619 Experiments and Validation

Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) Val495Ala mutant from Alcaligenes xylosoxidans

Single particle reconstruction
Overview of EMD-4619
Sample name: Quinol Dependent Nitric Oxide Reductase
Organisms: Achromobacter xylosoxidans, Alcaligenes xylosoxydans xylosoxydans
Fitted atomic model: 6qq6
Related EM entry by publication: EMD-4618

Map parameters

Recommended contour level: 0.039 (author)
Number of grid points: 200 × 200 × 200
Voxel size: 1.05 × 1.05 × 1.05 Å
Minimum density: -0.309
Maximum density: 0.441
Average density: 0.00
Standard deviation: 0.013

Sample information

Sample name: Quinol Dependent Nitric Oxide Reductase
Ligands: PROTOPORPHYRIN IX CONTAINING FE, FE (III) ION, CALCIUM ION, (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE, DODECYL-BETA-D-MALTOSIDE, water
Proteins: Quinol Dependent Nitric Oxide Reductase, Nitric oxide reductase subunit B

Validation information

Experimental information

 

Image processing

Applied symmetry: C2
Software: RELION
Number of particles: 227359

Fitting

Initial atomic model: 6QQ5
Fitting protocol: flexible
Refinement space: REAL

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 49.0
Nominal CS (mm): 2.70
Nominal magnification: 47710.0
Defocus max (nm): -3,000.00
Defocus min (nm): -1,200.00
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Acquisition
Number of images: 1803

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 5.00
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100
Details: Blot for 6 seconds with blot force of 6 prior to plunge freezing.