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Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in PBS pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.492 r_long_range_B_other 15.492 r_mcangle_it 8.888 r_mcangle_other 8.883 r_scangle_other 6.58 r_dihedral_angle_1_deg 6.111 r_dihedral_angle_3_deg 5.746 r_mcbond_it 5.071 r_mcbond_other 5.071 r_scbond_it 3.62
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.492 r_long_range_B_other 15.492 r_mcangle_it 8.888 r_mcangle_other 8.883 r_scangle_other 6.58 r_dihedral_angle_1_deg 6.111 r_dihedral_angle_3_deg 5.746 r_mcbond_it 5.071 r_mcbond_other 5.071 r_scbond_it 3.62 r_scbond_other 3.617 r_angle_refined_deg 1.242 r_angle_other_deg 0.471 r_chiral_restr 0.052 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg 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 FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 498395 Reported Resolution (Å) 2.17 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C2 Axial Rise 1.6 Angular Rotation 59.49
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.92 MODEL REFINEMENT Servalcat INITIAL EULER ASSIGNMENT RELION 5 FINAL EULER ASSIGNMENT RELION 5 CLASSIFICATION RELION 5 RECONSTRUCTION RELION 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1523940