☰ Navigation Tabs
Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C1 symmetry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PQ9 experimental model PDB 7ZLA
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.884 f_angle_d 0.591 f_chiral_restr 0.04 f_plane_restr 0.005 f_bond_d 0.003
Sample Binary complex between the PLP-bound homodimeric PdxR and a 48bp double strand DNA fragment
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 32628 Reported Resolution (Å) 3.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7PQ9, 7ZLA) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 142 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 120000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU 2.8 CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 1358491