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Crystal Structure of the S. cerevisiae glucokinase, Glk1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.4 293.15 2.4M Diammonium Phosphate, 0.1M CHES pH 9.4
Crystal Properties Matthews coefficient Solvent content 3.92 68.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.75 α = 90 b = 177.75 β = 90 c = 323.947 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M-F 2015-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.59 155.83 99.97 0.1003 0.1418 0.1003 0.988 8.28 2 61332 91.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.59 3.718 99.95 0.4831 0.6832 0.4831 0.638 1.56 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 1IG8 3.59 155.83 1.34 61322 3105 99.97 0.2685 0.2668 0.2709 0.3002 0.3007 85.05
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 20.2914 f_angle_d 1.4903 f_chiral_restr 0.0754 f_plane_restr 0.0062 f_bond_d 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22948 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling PHASER phasing