☰ Navigation Tabs
Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q8F YeiK PDB code 1Q8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 MPD, Sodium Acetate, ribose, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.466 α = 90 b = 84.062 β = 90 c = 112.483 γ = 90
Symmetry Space Group I 2 2 2
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 4 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 1.78 25 97.8 0.116 26.2 12.5 34056 34056 -3 -3 18
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 1.78 1.86 77.4 0.475 2.9 2669
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT YeiK PDB code 1Q8F 1.78 25 34056 34056 1086 97.8 0.1681 0.16811 0.16733 0.1627 0.19276 0.1874 RANDOM 17.623
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] 0.62 -0.79 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.275 r_scangle_it 4.618 r_scbond_it 2.862 r_mcangle_it 1.743 r_angle_refined_deg 1.305 r_mcbond_it 1 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.275 r_scangle_it 4.618 r_scbond_it 2.862 r_mcangle_it 1.743 r_angle_refined_deg 1.305 r_mcbond_it 1 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.072 r_metal_ion_refined 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2295 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing