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Cryo-EM reconstruction of a Staphylococcus aureus oleate hydratase (OhyA) assembly of dimers bound to a liposome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UR3
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.643 r_lrange_other 15.643 r_dihedral_angle_6_deg 15.284 r_dihedral_angle_3_deg 13.184 r_scangle_it 8.065 r_scangle_other 8.065 r_mcangle_it 7.051 r_mcangle_other 7.051 r_dihedral_angle_1_deg 4.484 r_scbond_it 4.431
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.643 r_lrange_other 15.643 r_dihedral_angle_6_deg 15.284 r_dihedral_angle_3_deg 13.184 r_scangle_it 8.065 r_scangle_other 8.065 r_mcangle_it 7.051 r_mcangle_other 7.051 r_dihedral_angle_1_deg 4.484 r_scbond_it 4.431 r_scbond_other 4.431 r_mcbond_it 4.102 r_mcbond_other 4.102 r_angle_refined_deg 1.073 r_dihedral_angle_2_deg 0.773 r_angle_other_deg 0.369 r_xyhbond_nbd_refined 0.221 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.182 r_nbd_refined 0.176 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.069 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_ncsr_local_group_4 0.003 r_ncsr_local_group_5 0.003 r_ncsr_local_group_6 0.003 r_ncsr_local_group_7 0.003 r_ncsr_local_group_8 0.003 r_ncsr_local_group_9 0.003 r_ncsr_local_group_16 0.003 r_ncsr_local_group_17 0.003 r_ncsr_local_group_18 0.003 r_ncsr_local_group_19 0.003 r_ncsr_local_group_20 0.003 r_ncsr_local_group_21 0.003 r_ncsr_local_group_30 0.003 r_ncsr_local_group_54 0.003 r_ncsr_local_group_55 0.003 r_ncsr_local_group_62 0.003 r_ncsr_local_group_63 0.003 r_ncsr_local_group_68 0.003 r_ncsr_local_group_69 0.003 r_ncsr_local_group_70 0.003 r_ncsr_local_group_73 0.003 r_ncsr_local_group_75 0.003 r_ncsr_local_group_76 0.003 r_ncsr_local_group_77 0.003 r_ncsr_local_group_79 0.003 r_ncsr_local_group_80 0.003 r_ncsr_local_group_81 0.003 r_ncsr_local_group_82 0.003 r_ncsr_local_group_84 0.003 r_ncsr_local_group_85 0.003 r_ncsr_local_group_2 0.002 r_ncsr_local_group_3 0.002 r_ncsr_local_group_10 0.002 r_ncsr_local_group_11 0.002 r_ncsr_local_group_14 0.002 r_ncsr_local_group_15 0.002 r_ncsr_local_group_22 0.002 r_ncsr_local_group_23 0.002 r_ncsr_local_group_26 0.002 r_ncsr_local_group_27 0.002 r_ncsr_local_group_28 0.002 r_ncsr_local_group_29 0.002 r_ncsr_local_group_31 0.002 r_ncsr_local_group_32 0.002 r_ncsr_local_group_33 0.002 r_ncsr_local_group_34 0.002 r_ncsr_local_group_35 0.002 r_ncsr_local_group_36 0.002 r_ncsr_local_group_37 0.002 r_ncsr_local_group_38 0.002 r_ncsr_local_group_39 0.002 r_ncsr_local_group_40 0.002 r_ncsr_local_group_41 0.002 r_ncsr_local_group_42 0.002 r_ncsr_local_group_43 0.002 r_ncsr_local_group_44 0.002 r_ncsr_local_group_45 0.002 r_ncsr_local_group_46 0.002 r_ncsr_local_group_47 0.002 r_ncsr_local_group_49 0.002 r_ncsr_local_group_51 0.002 r_ncsr_local_group_52 0.002 r_ncsr_local_group_53 0.002 r_ncsr_local_group_56 0.002 r_ncsr_local_group_58 0.002 r_ncsr_local_group_60 0.002 r_ncsr_local_group_61 0.002 r_ncsr_local_group_64 0.002 r_ncsr_local_group_66 0.002 r_ncsr_local_group_67 0.002 r_ncsr_local_group_71 0.002 r_ncsr_local_group_74 0.002 r_ncsr_local_group_78 0.002 r_ncsr_local_group_83 0.002 r_ncsr_local_group_86 0.002 r_ncsr_local_group_87 0.002 r_ncsr_local_group_88 0.002 r_ncsr_local_group_89 0.002 r_ncsr_local_group_90 0.002 r_gen_planes_other 0.001 r_ncsr_local_group_1 0.001 r_ncsr_local_group_12 0.001 r_ncsr_local_group_13 0.001 r_ncsr_local_group_24 0.001 r_ncsr_local_group_25 0.001 r_ncsr_local_group_48 0.001 r_ncsr_local_group_50 0.001 r_ncsr_local_group_57 0.001 r_ncsr_local_group_59 0.001 r_ncsr_local_group_65 0.001 r_ncsr_local_group_72 0.001 r_ncsr_local_group_91 0.001 r_bond_other_d
Sample Assembly of dimers of OhyA bound to a liposome
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 87806 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (8UR3) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 500 Maximum Defocus (nm) 2500 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 79000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4 MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC 4 FINAL EULER ASSIGNMENT cryoSPARC 4 CLASSIFICATION cryoSPARC 4 RECONSTRUCTION cryoSPARC 4 MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION