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Crystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 2-fluoroadenosine
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 8.5 291.5 0.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.254 α = 90 b = 112.079 β = 95.15 c = 100.451 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 2.42 100 91.9 0.0809 0.0809 10.52 74187 70373 2 35.92
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 2.42 2.49 79.54 0.406 0.406
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 PDB entry 3CE6 2.42 33.15 70373 70373 3728 91.91 0.19804 0.19373 0.1935 0.27993 0.2784 RANDOM 38.276
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] 2.49 0.33 -1.09 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 20.108 r_dihedral_angle_3_deg 17.656 r_dihedral_angle_1_deg 7.01 r_scangle_it 3.074 r_scbond_it 1.967 r_angle_refined_deg 1.699 r_mcangle_it 1.204 r_mcbond_it 0.702 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 20.108 r_dihedral_angle_3_deg 17.656 r_dihedral_angle_1_deg 7.01 r_scangle_it 3.074 r_scbond_it 1.967 r_angle_refined_deg 1.699 r_mcangle_it 1.204 r_mcbond_it 0.702 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.27 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.108 r_bond_refined_d 0.016 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 14996 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 256
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing