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1.9 Angstrom resolution crystal structure of a NAD synthetase (nadE) from Salmonella typhimurium LT2 in complex with NAD(+)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 protein in 300mM NaCl, 10mM Hepes Na pH 7.5, 0.5mM TCEP was mixed at 1:1 v/v ratio with NH4Sulphat 2M, Bis-Tris 0.1m pH 5.5, 10mm NAD-magic solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.97 58.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.82 α = 90 b = 91.82 β = 90 c = 75.05 γ = 120
Symmetry Space Group P 31 2 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 MARMOSAIC 300 mm CCD Be Lenses/Diamond Laue Mono 2009-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 29.06 99.7 13.7 10.1 29311 29311 -3 29.9
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 1.9 1.93 99.9 0.504 2.8 9.4 1350
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 29.06 27647 27647 1477 99.74 0.14611 0.14404 0.1866 0.2165 RANDOM 19.529
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] -0.4 -0.2 -0.4 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.611 r_dihedral_angle_4_deg 14.194 r_dihedral_angle_3_deg 9.838 r_dihedral_angle_1_deg 3.336 r_scangle_it 3.056 r_scbond_it 1.911 r_angle_refined_deg 1.374 r_mcangle_it 1.22 r_angle_other_deg 0.918 r_mcbond_it 0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.611 r_dihedral_angle_4_deg 14.194 r_dihedral_angle_3_deg 9.838 r_dihedral_angle_1_deg 3.336 r_scangle_it 3.056 r_scbond_it 1.911 r_angle_refined_deg 1.374 r_mcangle_it 1.22 r_angle_other_deg 0.918 r_mcbond_it 0.698 r_mcbond_other 0.196 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 84
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement XSCALE data scaling XDS data reduction XDS data scaling Structure phasing SHELXD phasing SHELXE model building Bp3 phasing SOLOMON phasing ARP model building WARP model building