☰ Navigation Tabs
Crystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Homocysteine Hydrolase in Ternary Complex with Substrate and Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291.5 0.2 M MgCl2, 0.1 M Tris pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties Matthews coefficient Solvent content 2.41 48.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.2 α = 90 b = 111.69 β = 96.01 c = 100.13 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC QUANTUM 315 mirrors 2008-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 1.2 99.5 58.8 0.309 2 384395 2 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) 1.19 1.23 3.1 0.677 0.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3CE6 2 30 114623 108886 5714 82.51 0.26405 0.26007 0.2597 0.34004 0.3374 RANDOM 35.22
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] -1.23 0.75 1.87 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.439 r_dihedral_angle_4_deg 18.852 r_dihedral_angle_3_deg 16.45 r_scangle_it 8.206 r_scbond_it 6.903 r_dihedral_angle_1_deg 6.514 r_mcangle_it 5.006 r_mcbond_it 3.961 r_angle_refined_deg 1.628 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.439 r_dihedral_angle_4_deg 18.852 r_dihedral_angle_3_deg 16.45 r_scangle_it 8.206 r_scbond_it 6.903 r_dihedral_angle_1_deg 6.514 r_mcangle_it 5.006 r_mcbond_it 3.961 r_angle_refined_deg 1.628 r_nbtor_refined 0.309 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14998 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement ADSC data collection d*TREK data reduction d*TREK data scaling CCP4 phasing