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Crystal structure of the C-terminal Hexokinase domain of human HK3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZT pdb entry 2NZT, chain A, residues 468 through 913
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 291 reservoir solution: 16% PEG 3350, 0.20 M Ammonium Citrate, 0.1 M HEPES. 0.005 M glucose-6-phosphate, 0.005 M ADP-Mg, 0.02 M TCEP, 1:100 (w/w) trypsin was added to the protein stock solution., pH 7.2, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.904 α = 90 b = 83.904 β = 90 c = 323.327 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 CCD ADSC QUANTUM 315 2009-03-20 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 20 98.4 53686
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 2.8 2.9 86.8 0.666
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 MR pdb entry 2NZT, chain A, residues 468 through 913 2.8 20 52939 1502 97.2 0.245 0.245 0.27 0.2409 69.23
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] 5.541 5.541 -11.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 12.304 r_dihedral_angle_3_deg 11.488 r_dihedral_angle_1_deg 3.864 r_angle_refined_deg 1.054 r_angle_other_deg 0.783 r_scangle_it 0.576 r_scbond_it 0.342 r_mcangle_it 0.137 r_mcbond_it 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 12.304 r_dihedral_angle_3_deg 11.488 r_dihedral_angle_1_deg 3.864 r_angle_refined_deg 1.054 r_angle_other_deg 0.783 r_scangle_it 0.576 r_scbond_it 0.342 r_mcangle_it 0.137 r_mcbond_it 0.07 r_chiral_restr 0.059 r_mcbond_other 0.03 r_bond_refined_d 0.011 r_bond_other_d 0.003 r_gen_planes_refined 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12521 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 112
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction