7SWY
2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 26.92 |
f_angle_d | 0.612 |
f_chiral_restr | 0.055 |
f_bond_d | 0.006 |
f_plane_restr | 0.004 |
Sample |
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40-601[TA-rich+1]-40 nucleosome |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 823685 |
Reported Resolution (Å) | 2.6 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (3LZ0) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | phenix.real_space_refine |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 49.9 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN 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 | 81000 |
Calibrated Magnification | 46296 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | Latitude | |
CTF CORRECTION | cryoSPARC | 3.2 |
MODEL FITTING | UCSF Chimera | |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.2 |
CLASSIFICATION | cryoSPARC | 3.2 |
RECONSTRUCTION | cryoSPARC | 3.2 |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF amplitude correction was performed following 3D reconstruction | 10900948 |