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Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 0.75M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, temperature 293K, FREE INTERFACE DIFFUSION, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.16 43.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.54 α = 90 b = 95.93 β = 120 c = 91.61 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 ADSC QUANTUM 315 2011-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL24XU SPring-8 BL24XU
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 0.93 79.35 93.5 0.126 0.87 12.2 5.3 883288 1
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 0.95 1 93.4 0.661 0.708 2.6 4.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RXY 0.93 29.66 834827 43368 95.9 0.15 0.149 0.1485 0.164 0.1598 RANDOM 8.86
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] -2.6 1.68 10.97 -8.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.628 r_sphericity_free 20.238 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 12.115 r_sphericity_bonded 7.518 r_dihedral_angle_1_deg 6.466 r_rigid_bond_restr 4.586 r_long_range_B_refined 2.049 r_long_range_B_other 2.049 r_angle_refined_deg 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.628 r_sphericity_free 20.238 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 12.115 r_sphericity_bonded 7.518 r_dihedral_angle_1_deg 6.466 r_rigid_bond_restr 4.586 r_long_range_B_refined 2.049 r_long_range_B_other 2.049 r_angle_refined_deg 1.69 r_scangle_other 1.64 r_scbond_it 1.423 r_scbond_other 1.423 r_mcangle_it 1.248 r_mcangle_other 1.248 r_mcbond_it 0.988 r_mcbond_other 0.988 r_angle_other_deg 0.919 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10834 Nucleic Acid Atoms Solvent Atoms 1092 Heterogen Atoms 158
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling