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Crystal structure of NAD kinase P101A mutant from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 294 50 mM Sodium Bromide, 150 mM tri-sodium citrate dihydrate, 14-16% w/v polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.042 α = 90 b = 119.174 β = 100.98 c = 67.593 γ = 90
Symmetry Space Group P 1 21 1
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 4 2006-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.04 66.355 99.6 0.109 0.119 0.048 11.2 6 58778 58778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.23 98.5 0.633 0.633 0.294 1.2 5.4 8470
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2I1W 2.12 34.776 0.03 58737 5887 99.44 0.2145 0.2116 0.2141 0.2685 0.2679 45.4889
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 13.751 f_angle_d 1.239 f_chiral_restr 0.065 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7866 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction