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Cryo-EM structure of L-lysine 6-dehydrogenase complex with NAD+ and L-lysine
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.564 r_dihedral_angle_4_deg 24.199 r_dihedral_angle_3_deg 15.014 r_long_range_B_refined 13.137 r_long_range_B_other 13.136 r_scangle_other 9.415 r_mcangle_it 5.593 r_mcangle_other 5.593 r_scbond_it 5.416 r_scbond_other 5.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.564 r_dihedral_angle_4_deg 24.199 r_dihedral_angle_3_deg 15.014 r_long_range_B_refined 13.137 r_long_range_B_other 13.136 r_scangle_other 9.415 r_mcangle_it 5.593 r_mcangle_other 5.593 r_scbond_it 5.416 r_scbond_other 5.416 r_dihedral_angle_1_deg 4.485 r_mcbond_it 3.36 r_mcbond_other 3.36 r_angle_other_deg 1.45 r_angle_refined_deg 1.207 r_chiral_restr 0.064 r_bond_other_d 0.033 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_refined_d 0.008 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 L-lysine 6-dehydrogenase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 672092 Reported Resolution (Å) 2.53 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
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 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 800 Maximum Defocus (nm) 1500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 4.0.1 MODEL REFINEMENT REFMAC 5.8.0267 RECONSTRUCTION RELION 4.0.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION