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Aeromonas hydrophila ExeD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQ7
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.08 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 8.649 r_mcangle_it 7.518 r_mcangle_other 7.518 r_mcbond_it 5.906 r_mcbond_other 5.906 r_long_range_B_refined 5.824 r_long_range_B_other 5.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.08 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 8.649 r_mcangle_it 7.518 r_mcangle_other 7.518 r_mcbond_it 5.906 r_mcbond_other 5.906 r_long_range_B_refined 5.824 r_long_range_B_other 5.824 r_scangle_other 5.694 r_scbond_other 4.41 r_scbond_it 4.409 r_angle_refined_deg 1.477 r_angle_other_deg 1.34 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
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 51960 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C15
Map-Model Fitting and Refinement Id 1 (5WQ7) Refinement Space REAL Refinement Protocol OTHER Refinement Target Cross-correlation coefficient Overall B Value 182 Fitting Procedure Details Coot and buccaneer for model building and refmac5 for refinement (CCPEM-1.1.0 suite).
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI POLARA 300 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode BRIGHT FIELD Specimen Holder Model GATAN LIQUID NITROGEN Nominal Magnification Calibrated Magnification 41322 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Latitude S CTF CORRECTION Gctf CTF CORRECTION RELION 2.1 MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION 2.1 FINAL EULER ASSIGNMENT RELION 2.1 CLASSIFICATION RELION 2.1 RECONSTRUCTION RELION 2.1 MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 272432