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Bifunctional dCTP deaminase: dUTPase from Mycobacterium tuberculosis in complex with dTTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XS1 PDB entry 1XS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 1.9 mg/ml enzyme in 20 mM MgCl2, 5mM dTTP, 50mM HEPES pH 6.8
reservoir solution: 45% PEG 400, 200mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 1.94 36.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.64 α = 70.75 b = 82.64 β = 70.75 c = 82.64 γ = 70.75
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 4 2006-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 19.6 98.1 0.159 15.01 22235 22235 -3 -3 22.025
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 2.1 97.8 0.595 4.5 2973
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1XS1 2 19.58 22234 22234 1112 100 0.164 0.164 0.161 0.1624 0.217 0.2146 RANDOM 16.975
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] 0.71 -1.08 -1.08 0.71 -1.08 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.765 r_dihedral_angle_4_deg 18.603 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 5.953 r_scangle_it 3.299 r_mcangle_it 2.995 r_scbond_it 2.434 r_mcbond_it 2.07 r_angle_refined_deg 1.378 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.765 r_dihedral_angle_4_deg 18.603 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 5.953 r_scangle_it 3.299 r_mcangle_it 2.995 r_scbond_it 2.434 r_mcbond_it 2.07 r_angle_refined_deg 1.378 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.25 r_symmetry_hbond_refined 0.238 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_metal_ion_refined 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2924 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 84
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction