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Bianthranilate-like inhibitor with 4-atom "line" and phosphonate "hook" fishing for hydrogen bond donors in Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QR9 PDB entry 3QR9 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.2 M imidazole-malate, 9% PEG-4000
Crystal Properties Matthews coefficient Solvent content 2.28 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.467 α = 90 b = 78.039 β = 111 c = 102.945 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2015-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 47 99.8 0.121 8.5 3.4 47170 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 97.7 0.856 1.5 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entry 3QR9 chain A 2 46.963 1.34 47156 2294 99.79 0.1937 0.1918 0.1945 0.2321 0.2338 Random selection
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 f_dihedral_angle_d 12.415 f_angle_d 0.774 f_chiral_restr 0.028 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4767 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 79
Software Software Software Name Purpose Blu-Ice data collection XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement