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Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1M Sodium Acetate, 25% PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.35 α = 90 b = 82.91 β = 112.15 c = 93.87 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 210 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 100 97.2 0.122 8.12 3.4 68457 68457 -3 30.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 95.4 0.388 3 3.2 4942
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1YOE 2.1 37.5 65238 65238 3455 98.02 0.20477 0.20477 0.20285 0.24093 0.2779 RANDOM 29.861
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] -2.04 -1.3 3.48 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.092 r_dihedral_angle_4_deg 14.886 r_dihedral_angle_3_deg 13.378 r_dihedral_angle_1_deg 6.459 r_scangle_it 3.28 r_scbond_it 2.141 r_angle_refined_deg 1.616 r_mcangle_it 1.296 r_mcbond_it 0.846 r_symmetry_hbond_refined 0.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.092 r_dihedral_angle_4_deg 14.886 r_dihedral_angle_3_deg 13.378 r_dihedral_angle_1_deg 6.459 r_scangle_it 3.28 r_scbond_it 2.141 r_angle_refined_deg 1.616 r_mcangle_it 1.296 r_mcbond_it 0.846 r_symmetry_hbond_refined 0.413 r_symmetry_vdw_refined 0.311 r_nbtor_refined 0.31 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.104 r_metal_ion_refined 0.026 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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_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 9119 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 71
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling