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Crystal structure of Hexokinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200mM Calcium acetate hydrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.57 α = 90 b = 77.52 β = 90 c = 108.73 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU 2018-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.987 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.72 50 99.57 0.098 0.021 22.8 7.6 61084 33.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.85 98.2 0.742 0.248 3.18 6.8
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 5HEX 1.72 37.17 1.36 61084 3090 99.58 0.1786 0.1772 0.1796 0.2057 0.2076 37.95
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 5.2595 f_angle_d 0.8477 f_chiral_restr 0.0517 f_bond_d 0.0063 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3536 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing