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X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 1.8 M ammonium citrate tribasic dihydrate, 5 % glycerol, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.13 α = 90 b = 178.13 β = 90 c = 215.177 γ = 90
Symmetry Space Group P 41 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.35 29.7 99.3 0.139 11.4 143290 142287 1 1 42.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 99 0.56 5.3 9636
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.35 29.7 143290 135143 7144 99.4 0.18743 0.18439 0.1866 0.24566 0.246 RANDOM 6.71
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.357 r_dihedral_angle_4_deg 18.982 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 7.02 r_scangle_it 2.669 r_angle_refined_deg 1.659 r_scbond_it 1.636 r_mcangle_it 0.968 r_mcbond_it 0.582 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.357 r_dihedral_angle_4_deg 18.982 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 7.02 r_scangle_it 2.669 r_angle_refined_deg 1.659 r_scbond_it 1.636 r_mcangle_it 0.968 r_mcbond_it 0.582 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20221 Nucleic Acid Atoms Solvent Atoms 1443 Heterogen Atoms 306
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing