7LXD
Structure of yeast DNA Polymerase Zeta (apo)
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6V8P |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.539 |
f_angle_d | 1.299 |
f_chiral_restr | 0.074 |
f_plane_restr | 0.009 |
f_bond_d | 0.006 |
Sample |
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DNA polymerase Zeta |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK II |
Cryogen Name | ETHANE |
Sample Vitrification Details | Blot for 6 seconds before plunging |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 213120 |
Reported Resolution (Å) | 4.11 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6V8P) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 45.7 |
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 | 48780 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | SerialEM | 3.9 |
CTF CORRECTION | cryoSPARC | 3.0 |
MODEL FITTING | UCSF Chimera | 1.14 |
MODEL REFINEMENT | PHENIX | 1.18.2-3874 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.0 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.0 |
CLASSIFICATION | cryoSPARC | 3.0 |
RECONSTRUCTION | cryoSPARC | 3.0 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 2974553 |