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Catalytic domain of GtfB in complex with inhibitor 2-[(2,4,5-Trihydroxyphenyl)methylidene]-1-benzofuran-3-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AIE The search model used was based on 3AIE of GtfC but using the GtfB sequence.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 2 M ammonium sulfate, 0.1 M Bis-Tris, apo- crystals soaked 5-10 mins with inhibitor HA5 (20 mM aqueous stock solution; 1-2 mM final concentration)
Crystal Properties Matthews coefficient Solvent content 4.42 72.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.455 α = 90 b = 150.455 β = 90 c = 304.948 γ = 90
Symmetry Space Group P 43 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 16M 2019-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.35 87.25 98.5 0.191 0.202 0.065 0.995 8.1 9.1 142674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 0.712 0.35 9.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3AIE 2.35 73.04 133011 6850 96.06 0.20675 0.20544 0.2083 0.23255 0.2362 RANDOM 57.9
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 14.348 r_long_range_B_refined 8.186 r_long_range_B_other 8.142 r_dihedral_angle_1_deg 7.402 r_scangle_other 5.705 r_mcangle_it 5.227 r_mcangle_other 5.227 r_scbond_it 3.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 14.348 r_long_range_B_refined 8.186 r_long_range_B_other 8.142 r_dihedral_angle_1_deg 7.402 r_scangle_other 5.705 r_mcangle_it 5.227 r_mcangle_other 5.227 r_scbond_it 3.82 r_scbond_other 3.615 r_mcbond_it 3.471 r_mcbond_other 3.471 r_angle_refined_deg 1.368 r_angle_other_deg 1.213 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13055 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 191
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing