6I1Y

Vibrio vulnificus EpsD


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other76.575
r_long_range_B_refined76.575
r_scangle_other67.24
r_scbond_other43.059
r_scbond_it43.058
r_mcangle_it38.684
r_mcangle_other38.684
r_dihedral_angle_2_deg27.407
r_mcbond_other26.257
r_mcbond_it26.256
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other76.575
r_long_range_B_refined76.575
r_scangle_other67.24
r_scbond_other43.059
r_scbond_it43.058
r_mcangle_it38.684
r_mcangle_other38.684
r_dihedral_angle_2_deg27.407
r_mcbond_other26.257
r_mcbond_it26.256
r_dihedral_angle_3_deg13.701
r_dihedral_angle_4_deg11.558
r_dihedral_angle_1_deg10.185
r_angle_refined_deg1.758
r_angle_other_deg1.245
r_chiral_restr0.068
r_gen_planes_refined0.031
r_gen_planes_other0.025
r_bond_refined_d0.013
r_bond_other_d
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_scangle_it
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Sample
EpsD
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles46126
Reported Resolution (Å)3.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC15
Map-Model Fitting and Refinement
Id1 (5WQ8)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetCross-correlation coefficient
Overall B Value146
Fitting Procedure
DetailsCoot and buccaneer for model building and refmac5 for refinement (CCPEM-1.1.0 suite).
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification
Calibrated Magnification41322
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLatitudeS
CTF CORRECTIONGctf
CTF CORRECTIONRELION2.1
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTRELION2.1
CLASSIFICATIONRELION2.1
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTREFMAC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION125884