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Crystal structure of human ketohexokinase complexed to different sugar molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HQQ PDB ENTRY 2HQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 291 0.7M ammonium sulphate, 0.5M lithium sulphate, 0.1M sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.69 66.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.264 α = 90 b = 107.823 β = 90 c = 146.679 γ = 90
Symmetry Space Group I 2 2 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 CCD ADSC QUANTUM 4 mirrors 2003-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 0.977 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.1 87.71 97.2 0.066 0.066 8.4 3.8 27885 27885 29.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 91.2 0.34 0.34 3.4 3.5 3744
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2HQQ 2.1 87.71 27885 26466 1416 96.78 0.19441 0.19263 0.1988 0.22777 0.2285 RANDOM 29.841
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] 0.22 1.35 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.728 r_dihedral_angle_4_deg 14.652 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_1_deg 5.365 r_scangle_it 2.132 r_mcangle_it 2.092 r_scbond_it 1.326 r_angle_refined_deg 1.292 r_mcbond_it 1.258 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.728 r_dihedral_angle_4_deg 14.652 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_1_deg 5.365 r_scangle_it 2.132 r_mcangle_it 2.092 r_scbond_it 1.326 r_angle_refined_deg 1.292 r_mcbond_it 1.258 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.287 r_symmetry_vdw_refined 0.253 r_xyhbond_nbd_refined 0.247 r_nbd_refined 0.224 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2277 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing