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Crystal structure of Kluyveromyces lactis glucokinase in complex with mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished model of closed KlGlk1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 droplet:
1:1 mixture of protein and reservoir
protein supplemented with:
9.8 mM mannose
9.8 mM DTT
reservoir solution:
1.6 M sodium malonate, pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.78 67.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.89 α = 90 b = 187.89 β = 90 c = 92.151 γ = 90
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 2016-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91840 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.35 46.97 100 0.994 7.4 6.6 66871 42.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 100 0.341 0.9 6.4
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 FOURIER SYNTHESIS FREE R-VALUE 2.35 42.01 1.34 66844 1645 99.97 0.192 0.1914 0.1917 0.2152 0.2158 53.44
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 12.8807 f_angle_d 0.4968 f_chiral_restr 0.0381 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7538 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 101
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling