4IXC

Crystal structure of Human Glucokinase in complex with a small molecule activator.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429220% 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 coefficientSolvent content
2.5451.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.628α = 90
b = 77.628β = 90
c = 85.824γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDRIGAKU SATURN 944mirrors2008-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1254.891.90.0789.95.8234425316322226.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0751.30.3091.71.843406

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT225.893443129871161391.440.189580.189580.186340.2491RANDOM40.426
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]
-1.27-1.272.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.826
r_dihedral_angle_4_deg18.748
r_dihedral_angle_3_deg15.494
r_dihedral_angle_1_deg6.495
r_angle_refined_deg1.871
r_angle_other_deg0.864
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.826
r_dihedral_angle_4_deg18.748
r_dihedral_angle_3_deg15.494
r_dihedral_angle_1_deg6.495
r_angle_refined_deg1.871
r_angle_other_deg0.864
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3457
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms46

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling