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MprF from Pseudomonas aeruginosa in GDN micelle, C2 symmetry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V35 in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.166 r_long_range_B_other 20.164 r_dihedral_angle_3_deg 15.548 r_scangle_other 13.747 r_mcangle_it 11.862 r_mcangle_other 11.86 r_scbond_it 7.61 r_scbond_other 7.609 r_mcbond_it 6.901 r_mcbond_other 6.9
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.166 r_long_range_B_other 20.164 r_dihedral_angle_3_deg 15.548 r_scangle_other 13.747 r_mcangle_it 11.862 r_mcangle_other 11.86 r_scbond_it 7.61 r_scbond_other 7.609 r_mcbond_it 6.901 r_mcbond_other 6.9 r_dihedral_angle_1_deg 4.745 r_dihedral_angle_2_deg 3.839 r_angle_refined_deg 0.746 r_angle_other_deg 0.247 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_4_deg 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
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 109157 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (4v35) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 146.5 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 28.75
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 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 13084 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 CTF CORRECTION RELION 4 MODEL FITTING Coot 0.9.8.8 MODEL FITTING UCSF Chimera 1.17.3 MODEL REFINEMENT PHENIX 1.20.1-4487 MODEL REFINEMENT REFMAC 5.8.0411 INITIAL EULER ASSIGNMENT RELION 4 FINAL EULER ASSIGNMENT cryoSPARC 4.3 CLASSIFICATION cryoSPARC 4.3 RECONSTRUCTION cryoSPARC 4.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1239668