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Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 3 [4-(3-([1,1'-Biphenyl]-3-yl)ureido)-2-hydroxybenzoic 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 5.5 293 0.1M Bis-Tris pH 5.5, 0.2M NH4-acetate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.93 36.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.04 α = 90 b = 87.53 β = 90 c = 98.22 γ = 90
Symmetry Space Group P 21 21 21
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 2014-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 2.7 66.04 96.9 0.131 9.1 5 15620 2.1 39.1
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 2.7 2.85 95.2 0.806 2.1 4.9
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 2.7 65.43 14795 782 96.07 0.21262 0.2097 0.2135 0.26632 0.2683 RANDOM 57.24
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] 3.5 -2.49 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.263 r_dihedral_angle_3_deg 18.361 r_dihedral_angle_4_deg 15.695 r_long_range_B_refined 9.992 r_long_range_B_other 9.991 r_mcangle_it 6.682 r_mcangle_other 6.681 r_dihedral_angle_1_deg 6.402 r_scangle_other 6.188 r_mcbond_it 4.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.263 r_dihedral_angle_3_deg 18.361 r_dihedral_angle_4_deg 15.695 r_long_range_B_refined 9.992 r_long_range_B_other 9.991 r_mcangle_it 6.682 r_mcangle_other 6.681 r_dihedral_angle_1_deg 6.402 r_scangle_other 6.188 r_mcbond_it 4.21 r_mcbond_other 4.196 r_scbond_it 3.768 r_scbond_other 3.768 r_angle_refined_deg 1.547 r_angle_other_deg 1.166 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 4444 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing