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Lipomyces starkeyi levoglucosan kinase bound to levoglucosan, ADP and magnesium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Equal volumes of reservoir buffer (19% PEG4000, 0.1 M sodium acetate, 0.1 M Tris pH 6.8) and LGK (7 mg/ml) in crystallization buffer (50 mM NaCl, 2 mM ADP, 4 mM MgCl2, 0.5 mM
TCEP, 1 mM aluminum nitrate, 10 mM sodium fluoride, 20 mM Tris pH 7.5) were mixed and a resulting
crystal was then soaked with 100 mM levoglucosan for 10
minutes.
Crystal Properties Matthews coefficient Solvent content 3.92 68.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.857 α = 90 b = 114.857 β = 90 c = 234.766 γ = 90
Symmetry Space Group P 41 21 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 RAYONIX MX-300 2013-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97945 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 47.57 99.9 0.101 9.1 3.9 145247
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.7 0.719 2.2 4.2
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 4YH5 1.8 47.057 1.33 145033 7286 99.78 0.1892 0.1877 0.189 0.2179 0.2182
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 13.722 f_angle_d 1.145 f_chiral_restr 0.08 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6641 Nucleic Acid Atoms Solvent Atoms 1001 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing