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Crystal structure of InhA in complex with 3-nitropropanoic acid inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 Purified protein incubated with NADH and 3NP in 5% (w/v) ethanol, 5% (w/v) MPD, 200mM sodium chloride, 100mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.39 α = 90 b = 96.39 β = 90 c = 139.5 γ = 120
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 MAR CCD 165 mm 2018-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLRI BEAMLINE BL7.2W 1.24 SLRI BL7.2W
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 2.5 28.76 99.9 0.086 8.3 2.6 50117
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 2.5 2.64 99.9 0.42 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6R9W 2.5 28.76 50088 2458 99.916 0.186 0.1847 0.1904 0.2195 0.2268 34.882
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] 0.081 0.041 0.081 -0.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.568 r_dihedral_angle_4_deg 17.598 r_dihedral_angle_3_deg 13.82 r_dihedral_angle_1_deg 6.139 r_lrange_it 2.731 r_lrange_other 2.696 r_scangle_it 1.259 r_scangle_other 1.259 r_mcangle_it 1.256 r_mcangle_other 1.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.568 r_dihedral_angle_4_deg 17.598 r_dihedral_angle_3_deg 13.82 r_dihedral_angle_1_deg 6.139 r_lrange_it 2.731 r_lrange_other 2.696 r_scangle_it 1.259 r_scangle_other 1.259 r_mcangle_it 1.256 r_mcangle_other 1.256 r_angle_refined_deg 1.173 r_angle_other_deg 1.095 r_mcbond_it 0.71 r_mcbond_other 0.71 r_scbond_it 0.701 r_scbond_other 0.701 r_nbd_other 0.216 r_symmetry_nbd_other 0.174 r_nbd_refined 0.17 r_nbtor_refined 0.146 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbd_refined 0.084 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7953 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing