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Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LPF
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.649 r_long_range_B_other 12.649 r_dihedral_angle_3_deg 11.395 r_scangle_other 9.8 r_mcangle_it 6.38 r_mcangle_other 6.38 r_dihedral_angle_1_deg 6.329 r_scbond_it 5.71 r_scbond_other 5.71 r_mcbond_it 3.968
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.649 r_long_range_B_other 12.649 r_dihedral_angle_3_deg 11.395 r_scangle_other 9.8 r_mcangle_it 6.38 r_mcangle_other 6.38 r_dihedral_angle_1_deg 6.329 r_scbond_it 5.71 r_scbond_other 5.71 r_mcbond_it 3.968 r_mcbond_other 3.967 r_dihedral_angle_2_deg 3.182 r_angle_refined_deg 0.809 r_angle_other_deg 0.336 r_chiral_restr 0.042 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 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 State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 5775 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry O
Map-Model Fitting and Refinement Id 1 (4LPF) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 106.4 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 27.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 12000 Maximum Defocus (nm) 35000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 75000 Calibrated Magnification 130841 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 CTF CORRECTION RELION MODEL FITTING UCSF Chimera 1.18 MODEL FITTING Coot 0.9.8.95 MODEL REFINEMENT REFMAC 5.8.0430 INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION CLASSIFICATION RELION RECONSTRUCTION RELION
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION