☰ Navigation Tabs
Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 6 [3-(3-(4-Bromophenyl)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 293 0.1 M MES pH 6.0, 0.2 M MgCl2, 25% (W/Vol) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.591 α = 94.33 b = 76.089 β = 108.32 c = 80.716 γ = 107.66
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 2014-10-16 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 2.57 75.25 97.9 0.158 4.4 2 42814 1.7
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 2.57 2.66 92.6 0.523 1.7 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 2.57 75.25 40602 2176 98.3 0.20445 0.20118 0.2076 0.26527 0.2729 RANDOM 32.716
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] -1.84 -0.38 -0.12 0.55 -1.22 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.508 r_dihedral_angle_4_deg 18.996 r_dihedral_angle_3_deg 16.756 r_dihedral_angle_1_deg 6.367 r_long_range_B_refined 5.758 r_long_range_B_other 5.758 r_scangle_other 2.952 r_mcangle_it 2.718 r_mcangle_other 2.718 r_scbond_it 1.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.508 r_dihedral_angle_4_deg 18.996 r_dihedral_angle_3_deg 16.756 r_dihedral_angle_1_deg 6.367 r_long_range_B_refined 5.758 r_long_range_B_other 5.758 r_scangle_other 2.952 r_mcangle_it 2.718 r_mcangle_other 2.718 r_scbond_it 1.807 r_scbond_other 1.807 r_mcbond_it 1.676 r_mcbond_other 1.676 r_angle_refined_deg 1.54 r_angle_other_deg 0.836 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 8771 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing