9T97 | pdb_00009t97

cryo-EM structure of AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.018
r_lrange_other17.018
r_dihedral_angle_6_deg15.931
r_dihedral_angle_3_deg11.946
r_scangle_it11.748
r_scangle_other11.748
r_mcangle_it8.525
r_mcangle_other8.525
r_scbond_it7.348
r_scbond_other7.348
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.018
r_lrange_other17.018
r_dihedral_angle_6_deg15.931
r_dihedral_angle_3_deg11.946
r_scangle_it11.748
r_scangle_other11.748
r_mcangle_it8.525
r_mcangle_other8.525
r_scbond_it7.348
r_scbond_other7.348
r_dihedral_angle_1_deg6.886
r_dihedral_angle_2_deg6.264
r_mcbond_it5.69
r_mcbond_other5.69
r_angle_refined_deg1.907
r_angle_other_deg0.631
r_ncsr_local_group_70.292
r_ncsr_local_group_50.235
r_ncsr_local_group_40.232
r_ncsr_local_group_30.227
r_ncsr_local_group_20.225
r_ncsr_local_group_10.223
r_ncsr_local_group_60.22
r_nbd_refined0.179
r_symmetry_nbd_other0.177
r_ncsr_local_group_150.156
r_nbtor_refined0.149
r_ncsr_local_group_80.128
r_ncsr_local_group_100.112
r_ncsr_local_group_140.11
r_ncsr_local_group_90.107
r_ncsr_local_group_130.105
r_ncsr_local_group_110.101
r_ncsr_local_group_120.094
r_chiral_restr0.088
r_xyhbond_nbd_refined0.08
r_symmetry_nbtor_other0.071
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.001
r_bond_other_d
Sample
AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles251974
Reported Resolution (Å)2.35
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)44.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2250
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.4.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC4.4.1
MODEL FITTINGUCSF ChimeraX1.10.1
MODEL REFINEMENTServalcat
INITIAL EULER ASSIGNMENTcryoSPARC4.4.1
FINAL EULER ASSIGNMENTcryoSPARC4.4.1
CLASSIFICATIONcryoSPARC4.4.1
RECONSTRUCTIONcryoSPARC4.4.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1279569