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Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3F PDB entry 1K3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 0.1M Na Acetate trihydrate, 10% PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.26 α = 90 b = 92.26 β = 90 c = 267.46 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH Capillary optics 2003-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54179
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 2.9 30 93 0.154 0.177 6.89 2.84 75053 26462 -0.2
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 2.9 2.95 75.9 0.338 0.333 3.05 2.79 1074
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1K3F 2.9 29.46 2 26462 1327 93.9 0.216 0.212 0.212 0.284 RANDOM 18.5
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 13.92 c_mcangle_it 11.79 c_scbond_it 10.41 c_mcbond_it 7.94 c_angle_deg 1.5 c_improper_angle_d 0.91 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11262 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement MAR345 data collection XDS data scaling MOLREP phasing