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Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 7 [3-(3-(4-Chlorophenyl)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 0.1M MES pH 6.0, 0.2 M MgCl2, 25% (W/Vol) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.301 α = 93.71 b = 75.849 β = 108.43 c = 79.303 γ = 107.87
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 mirrors 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 2.49 74.03 97.6 0.125 7.4 2.3 45415 2
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 2.49 2.58 90.2 0.533 2 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 2.49 74.03 43105 2290 97.59 0.20178 0.19873 0.205 0.25887 0.2591 RANDOM 34.772
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] -3.28 -0.16 -0.84 2.98 -1.9 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.96 r_dihedral_angle_3_deg 17.297 r_dihedral_angle_4_deg 16.387 r_dihedral_angle_1_deg 6.123 r_long_range_B_refined 5.876 r_long_range_B_other 5.876 r_scangle_other 3.049 r_mcangle_it 2.888 r_mcangle_other 2.888 r_scbond_it 1.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.96 r_dihedral_angle_3_deg 17.297 r_dihedral_angle_4_deg 16.387 r_dihedral_angle_1_deg 6.123 r_long_range_B_refined 5.876 r_long_range_B_other 5.876 r_scangle_other 3.049 r_mcangle_it 2.888 r_mcangle_other 2.888 r_scbond_it 1.853 r_scbond_other 1.853 r_mcbond_it 1.783 r_mcbond_other 1.783 r_angle_refined_deg 1.399 r_angle_other_deg 0.806 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 8837 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing