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Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 5 [3-(3-(p-Tolyl)ureido) benzoic acid]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.2M MgCl2, 0.1M MES pH 6, PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.57 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.552 α = 94.57 b = 76.373 β = 108.24 c = 80.865 γ = 107.65
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 2014-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91843 BESSY 14.1
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 1.64 47.7 96.9 0.031 12.9 2.4 163557 1.8 18.7
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 1.64 1.67 90.6 0.334 1.8 2.2
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 3DKI 1.64 47.47 155374 8180 96.93 0.16457 0.16343 0.1736 0.18606 0.1946 RANDOM 26.632
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] -1.55 0.06 -0.32 0.88 -0.85 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.27 r_dihedral_angle_4_deg 19.19 r_dihedral_angle_3_deg 13.354 r_long_range_B_refined 5.928 r_long_range_B_other 5.928 r_dihedral_angle_1_deg 5.555 r_scangle_other 3.76 r_mcangle_it 2.667 r_mcangle_other 2.666 r_scbond_it 2.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.27 r_dihedral_angle_4_deg 19.19 r_dihedral_angle_3_deg 13.354 r_long_range_B_refined 5.928 r_long_range_B_other 5.928 r_dihedral_angle_1_deg 5.555 r_scangle_other 3.76 r_mcangle_it 2.667 r_mcangle_other 2.666 r_scbond_it 2.404 r_scbond_other 2.403 r_mcbond_it 1.764 r_mcbond_other 1.764 r_angle_refined_deg 1.562 r_angle_other_deg 0.855 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8922 Nucleic Acid Atoms Solvent Atoms 892 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing