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X-ray structure of uridine nucleoside phosphorylease from Salmonella typhimurium complexed with phosphate and its inhibitor 2,2'-anhydrouridine at 1.86 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 295 PEG400, NaN3, GLYCEROL, PEG3350. K2HPO4, ANU, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.79 α = 90 b = 124.07 β = 90 c = 134.1 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 MAR CCD 165 mm 2004-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.85 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.86 88 88.4 0.094 124633 110180 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.86 1.87 93.6 0.506 2.49 1963
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DPS 1.86 27.99 104669 5509 88.44 0.17765 0.17615 0.20617 0.1917 RANDOM 20.376
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] 0.8 -0.3 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 15.724 r_dihedral_angle_3_deg 12.966 r_dihedral_angle_1_deg 5.596 r_scangle_it 1.922 r_scbond_it 1.072 r_angle_refined_deg 1.066 r_mcangle_it 0.819 r_mcbond_it 0.436 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 15.724 r_dihedral_angle_3_deg 12.966 r_dihedral_angle_1_deg 5.596 r_scangle_it 1.922 r_scbond_it 1.072 r_angle_refined_deg 1.066 r_mcangle_it 0.819 r_mcbond_it 0.436 r_nbtor_refined 0.294 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.145 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_refined 0.109 r_metal_ion_refined 0.099 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10965 Nucleic Acid Atoms Solvent Atoms 1015 Heterogen Atoms 66
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling