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Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with uridine and phosphate ion at 2.91A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.88 α = 90 b = 123.99 β = 90 c = 134.16 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 mirrors 2005-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8048 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.91 90.91 30842
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.909 2.985
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.91 90.91 30842 1650 97.7 0.21074 0.21074 0.2083 0.2036 0.25594 0.2111 RANDOM 5.932
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] -0.25 0.02 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.105 r_dihedral_angle_3_deg 15.19 r_dihedral_angle_4_deg 14.11 r_dihedral_angle_1_deg 5.051 r_angle_refined_deg 1.003 r_scangle_it 0.425 r_mcangle_it 0.381 r_nbtor_refined 0.293 r_scbond_it 0.229 r_mcbond_it 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.105 r_dihedral_angle_3_deg 15.19 r_dihedral_angle_4_deg 14.11 r_dihedral_angle_1_deg 5.051 r_angle_refined_deg 1.003 r_scangle_it 0.425 r_mcangle_it 0.381 r_nbtor_refined 0.293 r_scbond_it 0.229 r_mcbond_it 0.212 r_symmetry_vdw_refined 0.185 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11001 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement MOLREP phasing