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Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 50 mM EPPS, 100 mM MgCl2, 17.5%(w/v) PEG4000 (well solution); 10 mg/mL MtICL in 50 mM Tris pH 8.0, 100 mM NaCl, 5 mM MgSO4, 3 mM 3-nitropropionate, and 1 mM DTT (protein solution); 2 uL total drop volume, 1:1 well solution:protein solution
Crystal Properties Matthews coefficient Solvent content 2.18 43.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.76 α = 90 b = 87.13 β = 116.55 c = 152.99 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2017-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.2 47.393 98 0.198 0.2316 0.987 5.86 3.7 169258 33.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.279 99 1.63 1.903 0.377 0.77 3.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6C4A 2.2 47.393 1.33 169117 1999 98.44 0.1926 0.192 0.1959 0.2475 0.246 47.5217
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 12.258 f_angle_d 0.496 f_chiral_restr 0.038 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26436 Nucleic Acid Atoms Solvent Atoms 1597 Heterogen Atoms 103
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing