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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 1RKD PDB ENTRY 1RKD
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 3.75 67.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.26 α = 90 b = 109.619 β = 90 c = 146.29 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 2003-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.9795 SRS PX14.2
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 1.86 87.706 99.8 0.063 0.063 6.6 7.3 41681 41681 27.3
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) 1.86 1.96 99.2 0.325 0.325 5 7.3 6030
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Single Isomorphous Replacement THROUGHOUT PDB ENTRY 1RKD 1.86 87.71 41795 37359 4129 99.27 0.20768 0.20474 0.23384 0.2496 RANDOM 26.285
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] -0.02 1.38 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.599 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_3_deg 13.294 r_dihedral_angle_1_deg 5.434 r_mcangle_it 2.03 r_scangle_it 2.026 r_mcbond_it 1.764 r_scbond_it 1.349 r_angle_refined_deg 1.296 r_angle_other_deg 0.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.599 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_3_deg 13.294 r_dihedral_angle_1_deg 5.434 r_mcangle_it 2.03 r_scangle_it 2.026 r_mcbond_it 1.764 r_scbond_it 1.349 r_angle_refined_deg 1.296 r_angle_other_deg 0.702 r_mcbond_other 0.284 r_symmetry_vdw_other 0.27 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.212 r_nbd_other 0.203 r_symmetry_hbond_refined 0.2 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.132 r_nbtor_other 0.088 r_chiral_restr 0.075 r_xyhbond_nbd_other 0.065 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other 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 2277 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SOLVE phasing