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Crystal Structure of Trypanosoma brucei dUTPase with dUpNp and Ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DK4 PDB ENTRY 4DK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 20% w/v PEG3350, 0.2 M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.25 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.47 α = 90 b = 68.47 β = 90 c = 123.87 γ = 90
Symmetry Space Group P 43 21 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 QUANTUM 4 2010-06-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.831 48.416 100 0.11 0.11 18.5 13.7 26775 26775 1 1 20.1
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 1.831 1.93 100 0.584 0.584 1.3 13.1 3824
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4DK4 1.831 48.416 26675 26675 1331 99.86 0.1702 0.1702 0.1688 0.1978 0.2094 RANDOM 21.4041
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_scbond_it 28.336 r_scangle_it 24.393 r_dihedral_angle_3_deg 13.111 r_mcangle_it 12.524 r_mcbond_it 11.51 r_dihedral_angle_4_deg 10.979 r_dihedral_angle_1_deg 4.918 r_angle_refined_deg 1.44 r_angle_other_deg 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_scbond_it 28.336 r_scangle_it 24.393 r_dihedral_angle_3_deg 13.111 r_mcangle_it 12.524 r_mcbond_it 11.51 r_dihedral_angle_4_deg 10.979 r_dihedral_angle_1_deg 4.918 r_angle_refined_deg 1.44 r_angle_other_deg 0.95 r_mcbond_other 0.575 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1761 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 26
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection