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Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 3'-keto-aristeromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CE6 PDB entry 3CE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291.5 20% PEG 1000, 200 mM Imidazole pH 8.0, 100 mM Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.854 α = 90 b = 111.85 β = 96.49 c = 100.403 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 2005-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.96400 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.01 100 98.86 0.0671 0.0671 10.12 136379 129513 2 25.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.06 89.41 0.353 0.353
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3CE6 2.01 34.59 129513 129513 6853 98.86 0.19249 0.18961 0.2468 0.238 RANDOM 27.473
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] 2.17 -0.19 -1.17 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.003 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 14.915 r_scangle_it 7.57 r_dihedral_angle_1_deg 6.542 r_scbond_it 5.854 r_mcangle_it 4.086 r_mcbond_it 3.318 r_angle_refined_deg 1.568 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.003 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 14.915 r_scangle_it 7.57 r_dihedral_angle_1_deg 6.542 r_scbond_it 5.854 r_mcangle_it 4.086 r_mcbond_it 3.318 r_angle_refined_deg 1.568 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 14992 Nucleic Acid Atoms Solvent Atoms 844 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing