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Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in water
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 15.28 r_long_range_B_other 15.278 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_1_deg 9.683 r_mcangle_it 9.636 r_mcangle_other 9.632 r_scangle_other 9.044 r_mcbond_it 5.636 r_mcbond_other 5.636 r_scbond_it 4.739
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.28 r_long_range_B_other 15.278 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_1_deg 9.683 r_mcangle_it 9.636 r_mcangle_other 9.632 r_scangle_other 9.044 r_mcbond_it 5.636 r_mcbond_other 5.636 r_scbond_it 4.739 r_scbond_other 4.736 r_angle_refined_deg 1.342 r_angle_other_deg 0.422 r_chiral_restr 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 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 349067 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 2.39 Angular Rotation 179.24
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 crYOLO IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.92 INITIAL EULER ASSIGNMENT RELION 5 FINAL EULER ASSIGNMENT RELION 5 CLASSIFICATION RELION 5 RECONSTRUCTION RELION 5 MODEL REFINEMENT Servalcat
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1569255