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Crystal structure of Kluyveromyces lactis glucokinase mutant H304Q in complex with mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other intermediate refinement state of KlGlk1 in complex with mannose
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 6.3
Crystal Properties Matthews coefficient Solvent content 4.41 72.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.412 α = 90 b = 88.34 β = 89.92 c = 212.45 γ = 90
Symmetry Space Group I 1 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 PIXEL DECTRIS PILATUS 6M 2017-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.48 146.45 97.9 0.995 7.4 4 130184 69.98
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 2.48 2.52 98.8 0.285 0.5 4.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 2.48 64.28 1.33 129800 6451 97.49 0.2126 0.2114 0.2368 0.2317 90.42
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 12.9408 f_angle_d 0.6102 f_chiral_restr 0.0411 f_plane_restr 0.0047 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15072 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 181
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling