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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 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.81 α = 90 b = 83.24 β = 90 c = 51.57 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 optics 2005-06-18 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 2.1 107.2 97.5 0.067 14.4 7.2 54913 53540 3
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 2.1 2.154 96.1 0.276 6.2 7.4
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 2.1 65.68 52044 50785 2713 97.58 0.20273 0.20273 0.20014 0.1996 0.25155 0.2497 RANDOM 29.387
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] -1.63 -1.47 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 13.94 r_dihedral_angle_4_deg 13.739 r_dihedral_angle_1_deg 5.677 r_scangle_it 2.22 r_scbond_it 1.462 r_angle_refined_deg 1.263 r_mcangle_it 0.751 r_mcbond_it 0.446 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 13.94 r_dihedral_angle_4_deg 13.739 r_dihedral_angle_1_deg 5.677 r_scangle_it 2.22 r_scbond_it 1.462 r_angle_refined_deg 1.263 r_mcangle_it 0.751 r_mcbond_it 0.446 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5845 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling d*TREK data reduction CNS phasing