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cryo-EM structure of alligator haemoglobin in the T-like conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WIX
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 21.055 r_long_range_B_refined 21.054 r_scangle_other 15.804 r_dihedral_angle_3_deg 15.803 r_dihedral_angle_2_deg 13.044 r_mcangle_it 10.936 r_mcangle_other 10.932 r_scbond_it 10.26 r_scbond_other 10.218 r_mcbond_it 7.819
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 21.055 r_long_range_B_refined 21.054 r_scangle_other 15.804 r_dihedral_angle_3_deg 15.803 r_dihedral_angle_2_deg 13.044 r_mcangle_it 10.936 r_mcangle_other 10.932 r_scbond_it 10.26 r_scbond_other 10.218 r_mcbond_it 7.819 r_mcbond_other 7.787 r_dihedral_angle_1_deg 5.392 r_angle_refined_deg 1.747 r_angle_other_deg 0.597 r_chiral_restr 0.095 r_gen_planes_refined 0.011 r_bond_refined_d 0.009 r_gen_planes_other 0.007 r_bond_other_d 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
Sample alligator haemoglobin in carboxy form
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 238763 Reported Resolution (Å) 2.38 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (8WIX) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 1200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.2 MODEL REFINEMENT REFMAC 5.8.0419 CTF CORRECTION cryoSPARC 4.6.2 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 RECONSTRUCTION cryoSPARC 4.6.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION