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1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40 e/A^2 total dose)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N7X experimental model PDB 1MK5
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.9 r_lrange_other 26.775 r_lrange_it 26.566 r_dihedral_angle_4_deg 24.663 r_dihedral_angle_3_deg 14.664 r_scangle_it 10.92 r_scangle_other 10.913 r_mcangle_it 9.977 r_mcangle_other 9.972 r_dihedral_angle_1_deg 8.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.9 r_lrange_other 26.775 r_lrange_it 26.566 r_dihedral_angle_4_deg 24.663 r_dihedral_angle_3_deg 14.664 r_scangle_it 10.92 r_scangle_other 10.913 r_mcangle_it 9.977 r_mcangle_other 9.972 r_dihedral_angle_1_deg 8.687 r_scbond_it 7.11 r_scbond_other 7.102 r_mcbond_other 6.31 r_mcbond_it 6.309 r_angle_refined_deg 3.023 r_angle_other_deg 2.308 r_ext_dist_refined_d 0.41 r_nbtor_refined 0.1 r_nbd_refined 0.055 r_symmetry_nbd_other 0.05 r_symmetry_nbtor_other 0.04 r_nbd_other 0.04 r_chiral_restr 0.03 r_bond_refined_d 0.028 r_xyhbond_nbd_refined 0.028 r_symmetry_xyhbond_nbd_refined 0.028 r_bond_other_d 0.027 r_symmetry_nbd_refined 0.02 r_gen_planes_refined 0.001 r_gen_planes_other
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 153976 Reported Resolution (Å) 1.77 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D2
Map-Model Fitting and Refinement Id 1 (5N7X, 1MK5) Refinement Space RECIPROCAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 70
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1.13 MODEL FITTING MOLREP INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT REFMAC 5.8.0272
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION