Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Final map generated by local refinement in cryoSPARC using a soft mask encompassing MTCH2 only.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (8HBV)
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Real-space correlation coefficient
Overall B Value
136
Fitting Procedure
Details
Initial fitting was done using Coot and refined by Phenix cryo-EM real space refinement.
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
60
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.6
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
105000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.7.0
IMAGE ACQUISITION
SerialEM
CTF CORRECTION
cryoSPARC
4.7.0
MODEL FITTING
Coot
0.9.8.95
MODEL REFINEMENT
PHENIX
1.21.2_5419
INITIAL EULER ASSIGNMENT
cryoSPARC
4.7.0
FINAL EULER ASSIGNMENT
cryoSPARC
4.7.0
CLASSIFICATION
cryoSPARC
4.7.0
RECONSTRUCTION
cryoSPARC
4.7.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF parameters estimated using Patch CTF estimation in cryoSPARC. Global CTF correction for beam tilt was additionally performed.
4791546
14,190 out of 15,334 micrographs were selected for downstream processing. A total of 4,791,546 particles from blob picker and template picker were obtained. After running 11 rounds of heterogenous refinement, 485,622 particles were selected for further processing.