9QG9 | pdb_00009qg9

MDA phage capsid


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined33.346
r_long_range_B_other33.314
r_mcangle_it23.407
r_mcangle_other23.361
r_scangle_other21.943
r_dihedral_angle_3_deg14.977
r_mcbond_it13.47
r_mcbond_other13.428
r_scbond_it11.574
r_scbond_other11.539
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined33.346
r_long_range_B_other33.314
r_mcangle_it23.407
r_mcangle_other23.361
r_scangle_other21.943
r_dihedral_angle_3_deg14.977
r_mcbond_it13.47
r_mcbond_other13.428
r_scbond_it11.574
r_scbond_other11.539
r_dihedral_angle_1_deg9.427
r_angle_refined_deg1.581
r_angle_other_deg0.705
r_chiral_restr0.091
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_gen_planes_other0.004
r_bond_other_d0.001
r_dihedral_angle_2_deg
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
MDA
Specimen Preparation
Sample Aggregation StateHELICAL ARRAY
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles27134
Reported Resolution (Å)3.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC5
Axial Rise14.1313
Angular Rotation42.2769
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
DetailsPHENIX and Servalcat was used
Data Acquisition
Detector TypeTFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)41
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU
CTF CORRECTIONRELION4
MODEL FITTINGPHENIX
FINAL EULER ASSIGNMENTRELION4
RECONSTRUCTIONRELION4
MODEL REFINEMENTServalcat
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONRELION CTF Correction