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Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8A9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400
Crystal Properties Matthews coefficient Solvent content 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.898 α = 90 b = 74.279 β = 90 c = 118.386 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 PIXEL DECTRIS PILATUS 2M 2021-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.282 55.55 99.28 0.032 0.035 0.015 21.3 5.3 69703 25.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.592 1.619 1.085 0.44 7
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 FREE R-VALUE 1.59 55.55 1.34 69703 3439 97.03 0.18 0.1782 0.1785 0.2165 0.2173 39.69
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 15.3403 f_angle_d 0.8445 f_chiral_restr 0.0558 f_plane_restr 0.0057 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2078 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing PHENIX phasing