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Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZL2 PDB ENTRY 1ZL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 297 25% PEG 400, 0.1M potassium phosphate, 0.2M magnesium chloride, 0.1M cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.2 α = 90 b = 123.4 β = 90 c = 133.2 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 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 1.7 30 159741
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 1.7 1.74
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 PDB ENTRY 1ZL2 1.7 30 151618 7980 99.94 0.16742 0.1663 0.1653 0.18883 0.1881 RANDOM 8.391
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] -0.04 0.2 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.43 r_dihedral_angle_4_deg 15.326 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 5.558 r_sphericity_free 1.695 r_scangle_it 1.611 r_angle_refined_deg 1.067 r_scbond_it 0.972 r_sphericity_bonded 0.828 r_mcangle_it 0.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.43 r_dihedral_angle_4_deg 15.326 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 5.558 r_sphericity_free 1.695 r_scangle_it 1.611 r_angle_refined_deg 1.067 r_scbond_it 0.972 r_sphericity_bonded 0.828 r_mcangle_it 0.826 r_rigid_bond_restr 0.592 r_mcbond_it 0.491 r_nbtor_refined 0.299 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11116 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement MOLREP phasing