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Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O26 PDB ENTRY 1O26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 100mM Sodium acetate, 200mM potassium iodide, 2mM DTT and PEG3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.26 45.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.09 α = 90 b = 78.3 β = 96.8 c = 168.72 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 100 CCD ADSC QUANTUM 210 2004-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9794 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.013 44.95 96.1 0.096 11.4 3.4 132869 132869 20.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 89 0.474 3.1 2.9 12213
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 (All) 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 SAD in combination with Molecular Replacement THROUGHOUT PDB ENTRY 1O26 2.01 44.95 132869 126330 6506 95.47 0.1978 0.1978 0.19548 0.1973 0.24292 0.2449 RANDOM 24.695
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.286 r_dihedral_angle_4_deg 18.014 r_dihedral_angle_3_deg 14.934 r_dihedral_angle_1_deg 5.441 r_scangle_it 2.568 r_scbond_it 1.667 r_angle_refined_deg 1.293 r_mcangle_it 1.139 r_mcbond_it 0.681 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.286 r_dihedral_angle_4_deg 18.014 r_dihedral_angle_3_deg 14.934 r_dihedral_angle_1_deg 5.441 r_scangle_it 2.568 r_scbond_it 1.667 r_angle_refined_deg 1.293 r_mcangle_it 1.139 r_mcbond_it 0.681 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.16 r_metal_ion_refined 0.126 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15074 Nucleic Acid Atoms Solvent Atoms 989 Heterogen Atoms 686
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing AMoRE phasing