7XI9
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6X9I |
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 24.6331 |
f_angle_d | 0.632 |
f_chiral_restr | 0.0445 |
f_plane_restr | 0.0051 |
f_bond_d | 0.0039 |
Sample |
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DNMT1:H3Ub2:DNAmCG/fCGTernary complex of DNMT1 with hemi methylated DNA analog and H3Ub2 |
Sample Components |
DNA (cytosine-5)-methyltransferase 1 |
DNA |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Blot for 4 seconds before plunging |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 138662 |
Reported Resolution (Å) | 2.52 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6X9I, 6X9I, 6X9I) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | BACKBONE TRACE | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 49 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 1800 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 3.2.0 |
CTF CORRECTION | cryoSPARC | 3.2.0 |
MODEL FITTING | PHENIX | 1.17.1 |
MODEL REFINEMENT | PHENIX | 1.17.1 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
CLASSIFICATION | cryoSPARC | 3.2.0 |
RECONSTRUCTION | cryoSPARC | 3.2.0 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 3798046 |