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Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 22% PEG 2000MME, 0.3M sodium acetate, 0.1M TrisHCl, 8mM CHAPS, 10mM ATP, 2mM magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.93 α = 90 b = 83.29 β = 90 c = 51.42 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV++ osmic 2007-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 107.21 98.3 0.098 9.8 4.9 27719 27245 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.667 99.6 0.358 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.6 46.34 27719 27245 1450 98.29 0.21387 0.21387 0.21064 0.2122 0.2741 0.2759 RANDOM 35.827
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] -1.45 -2.07 3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_dihedral_angle_3_deg 16.515 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_1_deg 6.223 r_scangle_it 2.567 r_scbond_it 1.664 r_angle_refined_deg 1.591 r_mcangle_it 0.921 r_mcbond_it 0.564 r_symmetry_vdw_refined 0.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_dihedral_angle_3_deg 16.515 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_1_deg 6.223 r_scangle_it 2.567 r_scbond_it 1.664 r_angle_refined_deg 1.591 r_mcangle_it 0.921 r_mcbond_it 0.564 r_symmetry_vdw_refined 0.355 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.225 r_metal_ion_refined 0.191 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5806 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling d*TREK data reduction CNS phasing