9M2P | pdb_00009m2p

Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LPF 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined12.649
r_long_range_B_other12.649
r_dihedral_angle_3_deg11.395
r_scangle_other9.8
r_mcangle_it6.38
r_mcangle_other6.38
r_dihedral_angle_1_deg6.329
r_scbond_it5.71
r_scbond_other5.71
r_mcbond_it3.968
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined12.649
r_long_range_B_other12.649
r_dihedral_angle_3_deg11.395
r_scangle_other9.8
r_mcangle_it6.38
r_mcangle_other6.38
r_dihedral_angle_1_deg6.329
r_scbond_it5.71
r_scbond_other5.71
r_mcbond_it3.968
r_mcbond_other3.967
r_dihedral_angle_2_deg3.182
r_angle_refined_deg0.809
r_angle_other_deg0.336
r_chiral_restr0.042
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
Mycobacterium tuberculosis HisB, apo
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles5775
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryO
Map-Model Fitting and Refinement
Id1 (4LPF)
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value106.4
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)27.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)12000
Maximum Defocus (nm)35000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification130841
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.1
CTF CORRECTIONRELION
MODEL FITTINGUCSF Chimera1.18
MODEL FITTINGCoot0.9.8.95
MODEL REFINEMENTREFMAC5.8.0430
INITIAL EULER ASSIGNMENTRELION
FINAL EULER ASSIGNMENTRELION
CLASSIFICATIONRELION
RECONSTRUCTIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION