6FTX
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_other | 67.234 |
r_mcangle_it | 60.148 |
r_mcangle_other | 60.145 |
r_scbond_other | 43.08 |
r_scbond_it | 43.077 |
r_mcbond_other | 37.444 |
r_mcbond_it | 37.441 |
r_dihedral_angle_2_deg | 32.729 |
r_dihedral_angle_1_deg | 22.261 |
r_dihedral_angle_4_deg | 20.549 |
Sample |
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X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
Sample Components |
X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK III |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 135000 |
Reported Resolution (Å) | 4.5 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | 204 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 1.25 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 4000 |
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 | 35714 |
Calibrated Magnification | 35714 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | Gctf | |
MODEL FITTING | CCP4 package | |
INITIAL EULER ASSIGNMENT | RELION | |
FINAL EULER ASSIGNMENT | RELION | |
CLASSIFICATION | RELION | |
RECONSTRUCTION | RELION | |
MODEL REFINEMENT | REFMAC |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 860000 |