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Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila S2 cells
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 60%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.43 64.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.243 α = 90 b = 114.243 β = 90 c = 94.162 γ = 120
Symmetry Space Group P 32 2 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 MAR CCD 165 mm 2012-06-02 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 130 mm 2012-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1 SSRF BL17U 2 SYNCHROTRON BSRF BEAMLINE 1W2B 0.9793 BSRF 1W2B
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 1.9 50 99.75 50905 10.12 12.58
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 1.94 100
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD 1.952 49.469 1.34 50874 2570 98.08 0.1563 0.1549 0.1658 0.182 0.1915 RANDOM 20.5
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] -3.5447 -3.5447 7.0893
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.458 f_angle_d 1.253 f_chiral_restr 0.086 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3631 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection CNS refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing