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Cryo-EM structure of Apo coproheme decarboxylase from Corynebacterium diphtheria.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XUC
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.338 r_lrange_other 18.335 r_dihedral_angle_6_deg 17.483 r_dihedral_angle_3_deg 16.811 r_scangle_it 13.924 r_scangle_other 13.923 r_mcangle_it 10.794 r_mcangle_other 10.794 r_scbond_it 9.283 r_scbond_other 9.282
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.338 r_lrange_other 18.335 r_dihedral_angle_6_deg 17.483 r_dihedral_angle_3_deg 16.811 r_scangle_it 13.924 r_scangle_other 13.923 r_mcangle_it 10.794 r_mcangle_other 10.794 r_scbond_it 9.283 r_scbond_other 9.282 r_mcbond_it 7.896 r_mcbond_other 7.887 r_dihedral_angle_2_deg 5.503 r_dihedral_angle_1_deg 4.8 r_angle_refined_deg 1.254 r_angle_other_deg 0.406 r_xyhbond_nbd_refined 0.228 r_symmetry_nbd_other 0.208 r_nbd_refined 0.196 r_nbtor_refined 0.194 r_symmetry_xyhbond_nbd_other 0.104 r_ncsr_local_group_1 0.096 r_ncsr_local_group_6 0.095 r_ncsr_local_group_4 0.093 r_ncsr_local_group_10 0.091 r_ncsr_local_group_2 0.089 r_ncsr_local_group_9 0.089 r_ncsr_local_group_5 0.087 r_ncsr_local_group_7 0.086 r_ncsr_local_group_3 0.083 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_8 0.078 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d
Sample Structure of Apo coproheme decarboxylase from Corynebacterium diphtheria
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blotting time; 5.0-5.5 sec.
Blotting force; 18 or 19.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 638556 Reported Resolution (Å) 2.27 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C5
Map-Model Fitting and Refinement Id 1 (6XUC) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 72
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC MODEL FITTING MOLREP CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT REFMAC MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION