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Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5 291.15 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400
Crystal Properties Matthews coefficient Solvent content 2.26 45.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.79 α = 90 b = 75.62 β = 90 c = 118.11 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 2011-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933400 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.25 37.81 99.5 0.074 0.082 0.034 0.996 16.4 5.4 13690 30.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 97.9 0.48 0.548 0.254 0.79 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 MOLECULAR REPLACEMENT THROUGHOUT 2.25 37.39 1.34 13626 694 98.82 0.2075 0.2062 0.2065 0.2306 0.2307 40.71
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.2073 f_angle_d 0.689 f_chiral_restr 0.0551 f_bond_d 0.0083 f_plane_restr 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2075 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement PHENIX refinement MOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction PHENIX phasing