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Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with an inhibitor optimized from HTS lead
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 25 mM HEPES pH 7.5, 50 mM NaCl, 0.1 mM TCEP Reservoir:10% PEG 8000, 0.1M magnesium chloride, 0.1M HEPES pH 7.5 Cryo: 15% PEG 400 in reservoir solution, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.228 α = 90 b = 66.025 β = 90 c = 203.256 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2014-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.5 101.628 99.5 0.082 14 6.4 136219
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 1.5 1.505 96.6 0.319 5 6.7 1325
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 3TFT 1.5 101.628 136219 6602 99.44 0.187 0.1861 0.1856 0.2049 0.2043 RANDOM 15.528
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] -0.01 -0.31 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.68 r_dihedral_angle_4_deg 14.208 r_dihedral_angle_3_deg 13.103 r_dihedral_angle_1_deg 5.361 r_angle_refined_deg 1.089 r_chiral_restr 0.07 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6412 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing