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E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NUH
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.914 f_angle_d 0.573 f_chiral_restr 0.041 f_plane_restr 0.022 f_bond_d 0.004
Sample DNA binding and cleavage domain of the E. coli DNA Gyrase in State 1 Sample Components DNA binding and cleavage domain of the E. coli DNA Gyrase in State 1 DNA binding and cleavage domain of the E. coli DNA Gyrase in State 1 DNA binding and cleavage domain of the E. coli DNA Gyrase in State 1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 60548 Reported Resolution (Å) 4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (3NUH, 3NUH, 3NUH, 3NUH) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 300 Maximum Defocus (nm) 800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION RELION 2.0.3 MODEL FITTING UCSF Chimera 1.11.2 INITIAL EULER ASSIGNMENT cryoSPARC V1 FINAL EULER ASSIGNMENT RELION RECONSTRUCTION RELION 2.0.3 MODEL REFINEMENT PHENIX 1.12
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1572962