9W50 | pdb_00009w50

MprF from Pseudomonas aeruginosa mutant- H386C/F389C in nanodisc, C2 symmetry


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherD_1300050528 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined17.29
r_long_range_B_other17.29
r_dihedral_angle_3_deg14.639
r_scangle_other11.572
r_mcangle_it10.781
r_mcangle_other10.781
r_scbond_it6.434
r_scbond_other6.43
r_mcbond_it6.243
r_mcbond_other6.243
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined17.29
r_long_range_B_other17.29
r_dihedral_angle_3_deg14.639
r_scangle_other11.572
r_mcangle_it10.781
r_mcangle_other10.781
r_scbond_it6.434
r_scbond_other6.43
r_mcbond_it6.243
r_mcbond_other6.243
r_dihedral_angle_2_deg6.034
r_dihedral_angle_1_deg4.305
r_angle_refined_deg0.794
r_angle_other_deg0.308
r_chiral_restr0.04
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
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
Sample
MprF dimer
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles104195
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolOTHER
Refinement Target
Overall B Value142.6
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)26.7
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification130481
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONTopaz
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.1.14
CTF CORRECTIONRELION4
CTF CORRECTIONcryoSPARC4.5.3
MODEL FITTINGCoot0.9.8.8
MODEL FITTINGUCSF Chimera1.17.3
INITIAL EULER ASSIGNMENTRELION4
FINAL EULER ASSIGNMENTcryoSPARC4.5.3
CLASSIFICATIONRELION4
RECONSTRUCTIONcryoSPARC4.5.3
MODEL REFINEMENTPHENIX1.21.2-5419
MODEL REFINEMENTREFMAC5.8.0430
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION892429