7JPS
ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5UJM |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.033 |
f_angle_d | 1.139 |
f_chiral_restr | 0.06 |
f_plane_restr | 0.008 |
f_bond_d | 0.006 |
Sample |
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ORC-DNA |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 37734 |
Reported Resolution (Å) | 4.4 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5UJM, 5UJM, 5UJM, 5UJM, 5UJM) | 2 | |||
Refinement Space | REAL | REAL | |||
Refinement Protocol | RIGID BODY FIT | BACKBONE TRACE | |||
Refinement Target | Correlation Coefficient | ||||
Overall B Value | 231 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 66 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS 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 | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | Warp | 1.0.7 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | RELION | 3.0 |
MODEL FITTING | UCSF Chimera | |
INITIAL EULER ASSIGNMENT | cryoSPARC | 2 |
FINAL EULER ASSIGNMENT | RELION | 3.0 |
RECONSTRUCTION | RELION | 3.0 |
MODEL REFINEMENT | PHENIX | 1.18 |
MODEL REFINEMENT | Coot | 0.9 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 2097508 |