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Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 1 [3-(3-(3,4-Dichlorophenyl)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 5.5 293 0.2M MgCl2, 0.1M BT pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.479 α = 94.66 b = 76.044 β = 108.75 c = 81.627 γ = 107.29
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 2.08 47.7 97.3 0.065 9 2.9 80146 1.9 28
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 2.08 2.12 81 0.426 1.9 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DKI 2.08 75.8 76090 4051 97.27 0.17181 0.16984 0.20872 0.206 RANDOM 36.707
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] -1.7 -0.45 0.27 -0.21 -1.32 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.57 r_dihedral_angle_4_deg 17.501 r_dihedral_angle_3_deg 14.423 r_long_range_B_refined 6.222 r_long_range_B_other 5.987 r_dihedral_angle_1_deg 5.653 r_scangle_other 3.77 r_mcangle_it 3.041 r_mcangle_other 3.041 r_scbond_it 2.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.57 r_dihedral_angle_4_deg 17.501 r_dihedral_angle_3_deg 14.423 r_long_range_B_refined 6.222 r_long_range_B_other 5.987 r_dihedral_angle_1_deg 5.653 r_scangle_other 3.77 r_mcangle_it 3.041 r_mcangle_other 3.041 r_scbond_it 2.315 r_scbond_other 2.315 r_mcbond_it 1.94 r_mcbond_other 1.94 r_angle_refined_deg 1.359 r_angle_other_deg 0.805 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 8735 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing