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Human erythrocyte catalase cryoEM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F4J experimental model PDB 4BLC
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.422 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 13.556 r_long_range_B_refined 9.518 r_long_range_B_other 9.509 r_scangle_other 7.017 r_dihedral_angle_1_deg 6.993 r_mcangle_it 4.791 r_mcangle_other 4.791 r_scbond_it 4.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.422 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 13.556 r_long_range_B_refined 9.518 r_long_range_B_other 9.509 r_scangle_other 7.017 r_dihedral_angle_1_deg 6.993 r_mcangle_it 4.791 r_mcangle_other 4.791 r_scbond_it 4.301 r_scbond_other 4.301 r_mcbond_it 3.119 r_mcbond_other 3.118 r_angle_refined_deg 1.451 r_angle_other_deg 1.296 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 erythrocyte catalase with cofactors Heme and NADPH
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE Sample Vitrification Details Controlled environment plunge-freezer (Bellare et al, 1988; Technion University)
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 119169 Reported Resolution (Å) 2.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D2
Map-Model Fitting and Refinement Id 1 (1F4J, 4BLC) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 40 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 38
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) 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 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION RELION 3.1 MODEL FITTING Coot 9.03 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT REFMAC 5.8
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 150000 Autopicked using RELION Laplacian operator