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Human erythrocyte catalase with SLS as additive during cryo-EM grid preparation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DGF
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.255 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_1_deg 5.571 r_long_range_B_refined 5.239 r_long_range_B_other 5.239 r_mcangle_it 1.248 r_mcangle_other 1.248 r_angle_other_deg 1.246 r_angle_refined_deg 1.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.255 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_1_deg 5.571 r_long_range_B_refined 5.239 r_long_range_B_other 5.239 r_mcangle_it 1.248 r_mcangle_other 1.248 r_angle_other_deg 1.246 r_angle_refined_deg 1.179 r_scangle_other 0.677 r_mcbond_it 0.658 r_mcbond_other 0.658 r_scbond_it 0.313 r_scbond_other 0.313 r_chiral_restr 0.051 r_bond_other_d 0.03 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 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 Catalase purified from human erythrocytes
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot force, 0
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 33241 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D2
Map-Model Fitting and Refinement Id 1 (1dgf) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 151.4 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 33
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1800 Maximum Defocus (nm) 3000 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 130841 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 CTF CORRECTION RELION 3.1 MODEL FITTING UCSF Chimera 1.15 MODEL FITTING Coot 0.9.5 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.15 MODEL REFINEMENT REFMAC 5.8.0411
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION