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Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a thiazole inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein: 25 mM HEPES, 50 mM NaCl, 0.1 mM TCEP Reservoir:9% PEG 8000, 0.1M magnesium chloride, 0.1M HEPES Cryo: 15% PEG 400 in reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.34 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.039 α = 90 b = 66.237 β = 90 c = 204.239 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 193 CCD RIGAKU SATURN 944+ 2013-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.24 102.12 96.1 0.089 10.2 3.2 41863 41863
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.24 102.12 40217 2023 96.05 0.1719 0.1698 0.1697 0.2099 0.2059 RANDOM 20.714
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] -0.26 -0.28 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.625 r_dihedral_angle_4_deg 16.653 r_dihedral_angle_3_deg 14.159 r_dihedral_angle_1_deg 5.645 r_angle_refined_deg 1.351 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6387 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 102
Software Software Software Name Purpose StructureStudio data collection d*TREK data reduction d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing d*TREK data reduction d*TREK data scaling