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Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.793 r_long_range_B_refined 23.064 r_long_range_B_other 23.064 r_scangle_other 15.712 r_mcangle_it 13.938 r_mcangle_other 13.937 r_dihedral_angle_3_deg 12.167 r_dihedral_angle_4_deg 12.076 r_scbond_it 9.482 r_scbond_other 9.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.793 r_long_range_B_refined 23.064 r_long_range_B_other 23.064 r_scangle_other 15.712 r_mcangle_it 13.938 r_mcangle_other 13.937 r_dihedral_angle_3_deg 12.167 r_dihedral_angle_4_deg 12.076 r_scbond_it 9.482 r_scbond_other 9.482 r_mcbond_other 8.472 r_mcbond_it 8.471 r_dihedral_angle_1_deg 7.094 r_angle_refined_deg 1.491 r_angle_other_deg 1.023 r_chiral_restr 0.099 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.003 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
Sample Giant worm hemoglobin
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 75000 Reported Resolution (Å) 3.8 Resolution Method FSC 1/2 BIT CUT-OFF Other Details FSC as per the original definition (Harauz & van Heel 1986). Refinement Type Symmetry Type POINT Point Symmetry D6
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 1200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.02 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification 59000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION IMAGIC-4D IMAGE ACQUISITION EPU CTF CORRECTION IMAGIC-4D MODEL FITTING UCSF Chimera 1.11 MODEL REFINEMENT REFMAC 5.8.0155 MODEL REFINEMENT PHENIX 1.10.1 MODEL REFINEMENT Coot 0.8.6 INITIAL EULER ASSIGNMENT IMAGIC-4D FINAL EULER ASSIGNMENT IMAGIC-4D CLASSIFICATION IMAGIC-4D RECONSTRUCTION IMAGIC-4D
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY Unsupervised MSA classification of amplitude spectra throughout the full data set ("Full data set CTF correction") 319746