6FE8
Cryo-EM structure of the core Centromere Binding Factor 3 complex
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 50.886 |
r_long_range_B_other | 50.846 |
r_scangle_other | 41.658 |
r_dihedral_angle_2_deg | 30.625 |
r_mcangle_it | 30.386 |
r_mcangle_other | 30.384 |
r_scbond_it | 26.289 |
r_scbond_other | 26.287 |
r_mcbond_it | 18.689 |
r_mcbond_other | 18.683 |
Sample |
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The core Centromere Binding Factor 3 complex |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK I |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 69392 |
Reported Resolution (Å) | 4.1 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | 3D auto-refinement of all the good particles from 2D classification, provided a reconstruction at 4.7 angstrom overall resolution. After post-process ... |
Refinement Type | |
Symmetry Type | POINT |
Number of Particles | 187606 |
Reported Resolution (Å) | 3.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | 187, 606 particles were in the best two 3D classes. 3D auto-refinement of the 3D joined classes against the corresponding particles resulted in a fina ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (2VEQ, 1NEX) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 SUMMIT (4k x 4k) | GATAN K2 SUMMIT (4k x 4k) | |||||||
Electron Dose (electrons/Å**2) | 4.6 | 4.06 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
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 | |
Calibrated Magnification | 47170 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | Gautomatch | |
IMAGE ACQUISITION | EPU | 1.9.1 |
CTF CORRECTION | CTFFIND | 4.0 |
MODEL FITTING | UCSF Chimera | 1.8.1 |
MODEL FITTING | Coot | 0.8.8 |
MODEL REFINEMENT | PHENIX | 1.13 |
MODEL REFINEMENT | REFMAC | |
INITIAL EULER ASSIGNMENT | RELION | 2.0 |
FINAL EULER ASSIGNMENT | RELION | 2.0 |
CLASSIFICATION | RELION | 2.0 |
RECONSTRUCTION | RELION | 2.0 |
PARTICLE SELECTION | Gautomatch | |
CTF CORRECTION | CTFFIND | 4.0 |
INITIAL EULER ASSIGNMENT | RELION | 2.0 |
FINAL EULER ASSIGNMENT | RELION | 2.0 |
CLASSIFICATION | RELION | 2.0 |
RECONSTRUCTION | RELION | 2.0 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 139303 | |||
PHASE FLIPPING AND AMPLITUDE CORRECTION | 289281 |