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InhA Y158F mutant in complex with NADH from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 Thrombin cleaved InhA at 10 mg/ml with 3 to 10 mM of NADH was crystallized in a 24-well crystal plate, Combiclover Junior (Jena Bioscience). The best crystals appeared in drops of 2 ul of enzyme solution, 1 ul of the reservoir solution and 1 ul of distilled water. The reservoir solution contained 100 mM HEPES/NaOH pH 7.5, 50 mM sodium citrate pH 6.5, 7-9 % 2-methyl-2,4-pentanediol. Crystals appeared typically within two to three weeks in this condition.
Crystal Properties Matthews coefficient Solvent content 3.3 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.273 α = 90 b = 98.273 β = 90 c = 139.836 γ = 120
Symmetry Space Group P 62 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 CCD ADSC QUANTUM 315r 2016-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 1.07244 ESRF BM30A
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 1.8 46.61 100 0.065 0.067 0.015 1 35.6 20.5 37644
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 1.21 1.24 0.271 0.924 2.9 20.8
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 4TRO 1.8 42.553 1.34 37562 1884 99.9 0.1468 0.1454 0.1564 0.1751 0.1869
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 13.166 f_angle_d 1.129 f_chiral_restr 0.061 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1995 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing