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Crystal Structure of Trypanosoma brucei dUTPase with dUpNp, Ca2+ and Na+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGK PDB ENTRY 1OGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 25% w/v PEG1500, 0.1 M PCB buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.73 29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.84 α = 90 b = 83.19 β = 90 c = 91.18 γ = 90
Symmetry Space Group P 21 21 21
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 1.9 61.455 100 0.107 0.107 13.2 8.3 36008 36008 1 1 19.6
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 1.9 2 100 0.544 0.544 1.4 7.3 5150
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 1OGK 1.9 61.455 36008 35890 1793 99.82 0.1801 0.1801 0.1774 0.1825 0.2321 0.235 RANDOM 22.5685
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] -0.65 0.66 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.597 r_scbond_it 31.334 r_scangle_it 17.995 r_mcangle_it 15.028 r_dihedral_angle_4_deg 13.052 r_mcbond_it 12.662 r_dihedral_angle_3_deg 11.806 r_dihedral_angle_1_deg 5.28 r_angle_refined_deg 1.434 r_angle_other_deg 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.597 r_scbond_it 31.334 r_scangle_it 17.995 r_mcangle_it 15.028 r_dihedral_angle_4_deg 13.052 r_mcbond_it 12.662 r_dihedral_angle_3_deg 11.806 r_dihedral_angle_1_deg 5.28 r_angle_refined_deg 1.434 r_angle_other_deg 0.982 r_mcbond_other 0.413 r_chiral_restr 0.091 r_bond_refined_d 0.015 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 3364 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 54
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection