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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9D9U
pdb_00009d9u
10.2210/pdb9d9u/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Complex of marDK heterotetramer under dithionite reduced conditions
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3.5ul sample was applied to a glow discharged UltrAuFoil grid, blotted for 3 or 4 seconds before plunged in liquid ethane cooled with liquid nitrogen.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
149015
Reported Resolution (Å)
2.35
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Final step was actually Non-uniform Refinement of two classes of an Ab Initio reconstruction.
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
?
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å
2
)
50
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
2000
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
105000
Calibrated Magnification
109454
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Sample was screened using negative staining and Cryo-EM on a screening microscope for sample readiness assessment before automated high-throughput and high-resolution data collection on Titan Krios. Multiple batches of Cryo-EM specimen were prepared in order to deal with the orientation preference. The calibrated minimum/maximum defocus were the calculated minimum and maximum of images that with contaminants or broken ice.
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.2.1
IMAGE ACQUISITION
EPU
2.12
CTF CORRECTION
cryoSPARC
4.2.1
MODEL FITTING
PHENIX
?
MODEL REFINEMENT
PHENIX
?
MODEL REFINEMENT
ISOLDE
?
CLASSIFICATION
cryoSPARC
4.2.1
RECONSTRUCTION
cryoSPARC
4.2.1
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
