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Dimethylformamidase, 2x(A2B2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LVB
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.441 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_4_deg 11.908 r_dihedral_angle_1_deg 5.515 r_angle_refined_deg 1.236 r_angle_other_deg 1.107 r_long_range_B_refined 0.279 r_long_range_B_other 0.278 r_chiral_restr 0.044 r_bond_other_d 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.441 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_4_deg 11.908 r_dihedral_angle_1_deg 5.515 r_angle_refined_deg 1.236 r_angle_other_deg 1.107 r_long_range_B_refined 0.279 r_long_range_B_other 0.278 r_chiral_restr 0.044 r_bond_other_d 0.031 r_mcangle_it 0.023 r_mcangle_other 0.023 r_mcbond_it 0.012 r_mcbond_other 0.012 r_scangle_other 0.01 r_gen_planes_refined 0.004 r_scbond_it 0.004 r_scbond_other 0.004 r_bond_refined_d 0.003 r_gen_planes_other 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 DMFase, an amidohydrolase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details wait time - 10 seconds and 3.5 seconds blot
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 28964 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details The final reconstruction was from a single 3D class after B-factor weighting and aberration correction in Relion 3.1 Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (6LVB, 6LVB) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 73.98 Fitting Procedure Details Servalcat was used along with Refmac to calculate fofc maps and extensively used for modelling.
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 28.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 850 Maximum Defocus (nm) 3200 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 Gautomatch IMAGE ACQUISITION EPU 1.10 CTF CORRECTION Gctf 1.06 MODEL FITTING Coot 0.9.5 MODEL FITTING UCSF Chimera 1.15 MODEL REFINEMENT REFMAC 5.8.0267 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 114182