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Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 287 10% PEG 3000, 0.1 M Phosphate-citrate buffer, 0.2 M Sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.35 47.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.733 α = 90 b = 59.549 β = 106.01 c = 103.605 γ = 90
Symmetry Space Group P 1 21 1
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 315 2008-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97920 APS 19-ID
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 2.23 49.81 99.9 0.075 31.4 5.5 36765 36765 49.8
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 2.23 2.27 98.4 0.622 2.09 4.4 1789
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 SAD THROUGHOUT 2.23 49.81 36722 36722 1834 99.6 0.191 0.191 0.188 0.1922 0.237 0.2406 RANDOM 38.093
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] -1.06 -1.21 0.96 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.028 r_dihedral_angle_4_deg 21.095 r_dihedral_angle_3_deg 19.231 r_dihedral_angle_1_deg 6.402 r_scangle_it 3.273 r_scbond_it 2.206 r_angle_refined_deg 1.547 r_mcangle_it 1.398 r_mcbond_it 1.078 r_angle_other_deg 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.028 r_dihedral_angle_4_deg 21.095 r_dihedral_angle_3_deg 19.231 r_dihedral_angle_1_deg 6.402 r_scangle_it 3.273 r_scbond_it 2.206 r_angle_refined_deg 1.547 r_mcangle_it 1.398 r_mcbond_it 1.078 r_angle_other_deg 1.015 r_symmetry_vdw_other 0.285 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.208 r_nbd_other 0.203 r_mcbond_other 0.185 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.168 r_symmetry_hbond_refined 0.143 r_nbtor_other 0.093 r_chiral_restr 0.084 r_xyhbond_nbd_other 0.026 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5405 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing HKL-3000 phasing