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Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with 2,2'-anhydrouridine and phosphate ion at 1.85A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SJ9 PDB entry 1SJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 PEG 4000, SODIUM-ACETATE TRIHYDRATE, 2,2'-ANHYDROURIDINE, SODIUM PHOSPHATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.79 α = 90 b = 124.07 β = 90 c = 134.11 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 MARRESEARCH mirrors 2004-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.803 EMBL/DESY, HAMBURG X13
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 1.85 28.09 95.1 0.123 0.079 11.24 3.25 120586 14.4
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 1.85 1.97 96.2 0.399 0.36 3.55 3.25 20054
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1SJ9 1.85 28.09 2 120586 6010 95.1 0.179 0.178 0.178 0.1777 0.198 0.1975 RANDOM 25.2
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] 2.93 -1.09 -1.84
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 9.85 c_scbond_it 7.73 c_mcangle_it 6.41 c_mcbond_it 4.85 c_angle_deg 1.4 c_improper_angle_d 0.8 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10951 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 63
Software Software Software Name Purpose CNS refinement MAR345 data collection XDS data scaling MOLREP phasing