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Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-azido-5'-deoxyadenosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291.15 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.912 α = 90 b = 74.026 β = 90 c = 118.419 γ = 90
Symmetry Space Group I 2 2 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 210 2007-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934000 ESRF ID14-1
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 2.01 62.75 98.1 5.7 18364
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.12 94 5.6
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION Isomorphous replacement 2.0102 37.258 1.06 18364 556 96.79 0.187 0.1865 0.1873 0.2039 0.2039
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] 0.3822 11.8483 -12.2304
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.928 f_angle_d 0.84 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2043 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 61
Software Software Software Name Purpose ADSC data collection PHENIX refinement MOSFLM data reduction SCALA data scaling