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Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 22%(w/v) PEG2000MME, 0.1M TrisHCl pH 7.5 and 0.3M sodium acetate, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.2 α = 90 b = 83.6 β = 90 c = 51.6 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 CCD ADSC QUANTUM 4r mirrors 2003-08-27 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ osmic 2004-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.5362 NSLS X8C 2 ROTATING ANODE RIGAKU 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 71.73 98.8 0.093 21.9 26.94 63253 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 2.07 97.5 0.434 9.2 26.57 6169
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 SAD THROUGHOUT 2 107.83 63173 3148 98.79 0.215 0.214 0.2145 0.25 0.251 RANDOM 27.565
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] -1.53 -0.23 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.241 r_dihedral_angle_4_deg 15.694 r_dihedral_angle_3_deg 14.56 r_dihedral_angle_1_deg 5.723 r_scangle_it 2.27 r_scbond_it 1.558 r_angle_refined_deg 1.324 r_mcangle_it 0.841 r_mcbond_it 0.495 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.241 r_dihedral_angle_4_deg 15.694 r_dihedral_angle_3_deg 14.56 r_dihedral_angle_1_deg 5.723 r_scangle_it 2.27 r_scbond_it 1.558 r_angle_refined_deg 1.324 r_mcangle_it 0.841 r_mcbond_it 0.495 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.258 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.196 r_metal_ion_refined 0.165 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5917 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 87
Software Software Software Name Purpose d*TREK data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction SHELXDE phasing