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Lipomyces starkeyi levoglucosan kinase bound to levoglucosan
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 7 296 Equal amounts of LGK (9 mg/ml) in
50 mM NaCl, 0.5 mM TCEP, 20 mM Tris pH 7.5 and 200 mM levoglucosan were mixed with reservoir buffer containing 1.8 M ammonium sulfate, 0.1 M HEPES 7.0 and 0.1 M sodium acetate.
Crystal Properties Matthews coefficient Solvent content 3.3 62.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.32 α = 90 b = 70.32 β = 90 c = 263.334 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 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 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 1.85 48.86 100 0.096 9.8 5.6 57761
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 1.85 1.95 100 0.861 1.9 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YH5 1.85 48.86 1.34 57602 2897 99.88 0.1949 0.1937 0.2192 0.2112 Random selection
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 14.385 f_angle_d 1.035 f_chiral_restr 0.07 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3300 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing