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The crystal structure of native Trypanosoma cruzi dUTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other LOW RESOLUTION MAD STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 15% PEG 2000 MME, 0.1 M LISO4, 50 MM SODIUM CACODYLATE PH 6.6
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.434 α = 90 b = 136.434 β = 90 c = 68.705 γ = 120
Symmetry Space Group P 63 2 2
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 CCD MIRRORS 2000-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.4 12 97.5 0.05 32.4 7.2 14827
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 2.4 2.44 88.4 0.41 4.1 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MAD THROUGHOUT LOW RESOLUTION MAD STRUCTURE 2.4 30 14099 724 96.8 0.206 0.203 0.2352 0.263 0.2701 RANDOM 29.7
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_1_deg 6.427 r_scangle_it 3.931 r_scbond_it 2.369 r_mcangle_it 1.648 r_angle_refined_deg 1.542 r_angle_other_deg 0.906 r_mcbond_it 0.856 r_symmetry_vdw_other 0.235 r_nbd_other 0.228 r_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.427 r_scangle_it 3.931 r_scbond_it 2.369 r_mcangle_it 1.648 r_angle_refined_deg 1.542 r_angle_other_deg 0.906 r_mcbond_it 0.856 r_symmetry_vdw_other 0.235 r_nbd_other 0.228 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.203 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.107 r_nbtor_other 0.096 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2003 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing MLPHARE phasing AMoRE phasing