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Crystals structure of Human Glucokinase in complex with small molecule activator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V4S PDB ENTRY 1V4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 292 20% glucose, 10-18% Peg8000, 200mM sodium acetate, MMT 100mM pH7.0-8.5, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.938 α = 90 b = 77.938 β = 90 c = 85.35 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 200 CCD RIGAKU SATURN 944 Osmic VariMax HF mirrors 2008-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 55 95.2 0.052 10.6 2.43 29845 28409 2 2 27.84
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 2.1 2.18 73.4 0.275 2 2.1 2825
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1V4S 2.1 37.46 29845 26853 1450 94.83 0.20165 0.20165 0.19897 0.24982 0.2433 RANDOM 44.59
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] -1.08 -1.08 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.703 r_dihedral_angle_4_deg 21.455 r_dihedral_angle_3_deg 16.662 r_dihedral_angle_1_deg 6.787 r_angle_refined_deg 1.854 r_angle_other_deg 0.888 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.703 r_dihedral_angle_4_deg 21.455 r_dihedral_angle_3_deg 16.662 r_dihedral_angle_1_deg 6.787 r_angle_refined_deg 1.854 r_angle_other_deg 0.888 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3457 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 46
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling