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X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine at 2.38a resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 PEG400, NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.37 α = 90 b = 125.308 β = 90 c = 135.177 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 CCD MAR CCD 165 mm mirrors 2006-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 1.0500 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 2.38 20 61088
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.38 19.94 59239 1849 98.39 0.20944 0.20794 0.25787 0.2267 RANDOM 34.733
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.5 r_dihedral_angle_4_deg 15.996 r_dihedral_angle_3_deg 14.026 r_dihedral_angle_1_deg 5.026 r_angle_refined_deg 1.154 r_scangle_it 0.872 r_scbond_it 0.529 r_mcangle_it 0.498 r_nbtor_refined 0.288 r_mcbond_it 0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.5 r_dihedral_angle_4_deg 15.996 r_dihedral_angle_3_deg 14.026 r_dihedral_angle_1_deg 5.026 r_angle_refined_deg 1.154 r_scangle_it 0.872 r_scbond_it 0.529 r_mcangle_it 0.498 r_nbtor_refined 0.288 r_mcbond_it 0.284 r_nbd_refined 0.166 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_refined 0.129 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.076 r_bond_refined_d 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11005 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 96
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction