☰ Navigation Tabs
cryo-EM structure of human haemoglobin in oxy form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DN1
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.682 r_dihedral_angle_3_deg 21.779 r_long_range_B_other 19.864 r_long_range_B_refined 19.84 r_scangle_other 14.39 r_mcangle_it 9.897 r_mcangle_other 9.897 r_scbond_it 9.576 r_scbond_other 9.514 r_mcbond_it 7.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.682 r_dihedral_angle_3_deg 21.779 r_long_range_B_other 19.864 r_long_range_B_refined 19.84 r_scangle_other 14.39 r_mcangle_it 9.897 r_mcangle_other 9.897 r_scbond_it 9.576 r_scbond_other 9.514 r_mcbond_it 7.266 r_mcbond_other 7.241 r_dihedral_angle_1_deg 6.14 r_angle_refined_deg 1.845 r_angle_other_deg 0.612 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 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 human haemoglobin in oxy 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 550843 Reported Resolution (Å) 2.27 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (2dn1) 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