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Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine derivative
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 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.61 α = 90 b = 75.43 β = 90 c = 118.34 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 315r 2011-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939274 ESRF ID14-4
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 2.29 55.34 91.9 0.074 0.082 0.034 0.996 15.8 5.7 11859 36.22
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 2.29 2.37 98.6 0.584 0.639 0.254 0.942 5.9
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 2.29 34.96 1.34 11833 570 91.15 0.1907 0.1889 0.1913 0.2278 0.23 42.43
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 19.6234 f_angle_d 0.6144 f_chiral_restr 0.0465 f_plane_restr 0.0031 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2068 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement PHENIX refinement MOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction PHENIX phasing