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The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NATIVE STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 25% PEG 2000 MME, 0.3M SODIUM FORMATE, 50 MM SODIUM HEPES PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.3 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.386 α = 90 b = 50.307 β = 101.35 c = 111.387 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 CCD MIRRORS 2001-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.85 20 99.7 0.085 9.46 3.5 27211
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 2.85 2.9 97.3 0.442 1.1 3
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 MOLECULAR REPLACEMENT THROUGHOUT NATIVE STRUCTURE 2.85 111.8 25841 1362 99.1 0.209 0.205 0.2096 0.273 0.2673 RANDOM 34.97
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] -4.7 1.18 4.15 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.222 r_scangle_it 2.78 r_angle_refined_deg 1.931 r_scbond_it 1.618 r_mcangle_it 1.247 r_angle_other_deg 1.019 r_mcbond_it 0.65 r_symmetry_vdw_other 0.257 r_nbd_other 0.25 r_nbd_refined 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.222 r_scangle_it 2.78 r_angle_refined_deg 1.931 r_scbond_it 1.618 r_mcangle_it 1.247 r_angle_other_deg 1.019 r_mcbond_it 0.65 r_symmetry_vdw_other 0.257 r_nbd_other 0.25 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.151 r_nbtor_other 0.101 r_chiral_restr 0.094 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 7712 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing