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cryo-EM structure of alligator haemoglobin in oxy form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.608 r_long_range_B_refined 19.362 r_long_range_B_other 19.325 r_scangle_other 13.877 r_scbond_it 9.001 r_scbond_other 8.984 r_mcangle_other 8.216 r_mcangle_it 8.211 r_dihedral_angle_2_deg 7.003 r_dihedral_angle_1_deg 5.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.608 r_long_range_B_refined 19.362 r_long_range_B_other 19.325 r_scangle_other 13.877 r_scbond_it 9.001 r_scbond_other 8.984 r_mcangle_other 8.216 r_mcangle_it 8.211 r_dihedral_angle_2_deg 7.003 r_dihedral_angle_1_deg 5.826 r_mcbond_it 5.643 r_mcbond_other 5.642 r_angle_refined_deg 1.842 r_angle_other_deg 0.611 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 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 372582 Reported Resolution (Å) 2.31 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 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 FEI TITAN 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 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.2.1 MODEL FITTING Coot 0.9.8.8 MODEL FITTING ISOLDE 1.6 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL REFINEMENT Servalcat 0.2.85 INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION