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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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.78 α = 90 b = 83.53 β = 90 c = 51.24 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 2005-06-17 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 2.2 106.6 98.9 0.08 17.3 13.7 45236 44738 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 2.2 2.257 95.5 0.302 8 12.74
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 2.2 65.82 45236 44738 2385 98.87 0.2012 0.2012 0.19872 0.1981 0.24883 0.2465 RANDOM 32.791
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] -1.1 -1.14 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.665 r_dihedral_angle_3_deg 14.91 r_dihedral_angle_4_deg 12.767 r_dihedral_angle_1_deg 5.665 r_scangle_it 2.182 r_scbond_it 1.472 r_angle_refined_deg 1.404 r_mcangle_it 0.779 r_mcbond_it 0.443 r_symmetry_hbond_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.665 r_dihedral_angle_3_deg 14.91 r_dihedral_angle_4_deg 12.767 r_dihedral_angle_1_deg 5.665 r_scangle_it 2.182 r_scbond_it 1.472 r_angle_refined_deg 1.404 r_mcangle_it 0.779 r_mcbond_it 0.443 r_symmetry_hbond_refined 0.345 r_nbtor_refined 0.303 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.145 r_chiral_restr 0.095 r_metal_ion_refined 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5769 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling d*TREK data reduction CNS phasing