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Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 2 [3-(3-([1,1'-biphenyl]-3-yl)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 NH4-acetate, 0.1M BT pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.17 α = 90 b = 86.487 β = 90 c = 101.584 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 1.73 65.86 98.3 0.041 19.6 4.5 65578 2 25.7
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 1.73 1.81 98.8 0.717 2 4.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3dki 1.73 65.85 62228 3308 97.81 0.17549 0.17381 0.20671 0.2054 RANDOM 33.351
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] 2.99 -1.61 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.092 r_dihedral_angle_4_deg 18.162 r_dihedral_angle_3_deg 13.702 r_long_range_B_refined 5.961 r_long_range_B_other 5.961 r_dihedral_angle_1_deg 5.825 r_scangle_other 4.52 r_mcangle_it 3.201 r_mcangle_other 3.201 r_scbond_it 3.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.092 r_dihedral_angle_4_deg 18.162 r_dihedral_angle_3_deg 13.702 r_long_range_B_refined 5.961 r_long_range_B_other 5.961 r_dihedral_angle_1_deg 5.825 r_scangle_other 4.52 r_mcangle_it 3.201 r_mcangle_other 3.201 r_scbond_it 3.009 r_scbond_other 3.009 r_mcbond_it 2.361 r_mcbond_other 2.287 r_angle_refined_deg 1.608 r_angle_other_deg 0.873 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 4682 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing