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Structure of NP459575, a predicted glutathione synthase from Salmonella typhimurium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 Drop- 50 mM Na cacodylate pH 6.5, 5 mM Tris pH 8.3, 0.125 M NaCl, 0.1 M MgS, 10 % PEG 4000, 5 mg/ml protein. Well- 0.1 M Na cacodylate pH 6.5, 0.2 M MgS, 20 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.2 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.929 α = 90 b = 188.929 β = 90 c = 188.929 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 CCD CUSTOM-MADE 2004-04-03 M SIRAS 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.00800 APS 19-ID 2 SYNCHROTRON APS BEAMLINE 19-ID 1.0725 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 2.8 30 100 0.084 30 15 27578 -3 69
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 2.8 2.9 100 0.314 9.8 15 2714
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 SIRAS THROUGHOUT 2.801 19.92 27578 26187 1391 95 0.21132 0.21132 0.20884 0.2026 0.25768 0.2537 RANDOM 46.081
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.635 r_dihedral_angle_1_deg 6.397 r_scbond_it 4.674 r_mcangle_it 3.652 r_mcbond_it 2.294 r_angle_other_deg 1.179 r_angle_refined_deg 1.176 r_nbd_other 0.242 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.212
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.635 r_dihedral_angle_1_deg 6.397 r_scbond_it 4.674 r_mcangle_it 3.652 r_mcbond_it 2.294 r_angle_other_deg 1.179 r_angle_refined_deg 1.176 r_nbd_other 0.242 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.195 r_metal_ion_refined 0.115 r_symmetry_hbond_refined 0.106 r_nbtor_other 0.085 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5543 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing