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Uridine Phosphorylase from E. coli, Refined in the Monoclinic Crystal Lattice
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other trigonal form of Upase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 drops-0.05 M Tris-HCl and 4-6% PEG 4000; equilibrium solution-0.1M Tris-mal/NaOH pH5.91-5.96, 20-25% Peg 4000 and 0.04% sodium azide, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.6 α = 90 b = 98.8 β = 120.2 c = 93.7 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 293 DIFFRACTOMETER KARD-6 1994-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER
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 2.5 40 84 0.097 50479 42403 2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT trigonal form of Upase 2.5 6 2 50479 42401 0.186 0.186 random
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 x_angle_d 2.095 x_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11286 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing X-PLOR refinement