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Crystal structure of Trypanosoma brucei nucleoside phosphorylase shows uridine phosphorylase activity
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 39% PEG 8000, 0.1 M Tris-HCl pH 8.5, 0.1 M Sodium phosphate monobasic, 10 mM Uridine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 49.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.015 α = 90 b = 95.387 β = 105.91 c = 63.483 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 MARMOSAIC 325 mm CCD Mirrors 2007-03-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91724, 0.97910, 0.91160 SSRL BL9-2
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 1.44 40 95.4 0.079 8.4 3.4 123263 123263 15.8
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 1.44 1.5 73.4 0.637 1.2 2.4 9430
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.44 35.38 123193 123193 6191 94.72 0.156 0.156 0.155 0.1575 0.184 0.1855 RANDOM 16.915
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] -0.92 -0.62 -0.4 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.398 r_dihedral_angle_4_deg 16.468 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 5.856 r_scangle_it 4.3 r_scbond_it 2.948 r_mcangle_it 2.267 r_mcbond_it 1.722 r_angle_refined_deg 1.325 r_angle_other_deg 0.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.398 r_dihedral_angle_4_deg 16.468 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 5.856 r_scangle_it 4.3 r_scbond_it 2.948 r_mcangle_it 2.267 r_mcbond_it 1.722 r_angle_refined_deg 1.325 r_angle_other_deg 0.867 r_mcbond_other 0.477 r_symmetry_vdw_other 0.227 r_nbd_refined 0.208 r_nbd_other 0.203 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.095 r_nbtor_other 0.083 r_chiral_restr 0.072 r_symmetry_vdw_refined 0.072 r_metal_ion_refined 0.048 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4984 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 45
Software Software Software Name Purpose Blu-Ice data collection DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling