3A0I

Human glucokinase in complex with a synthetic activator


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V4SPDB ENTRY 1V4S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.629830 % PEG 1500, HEPES, PH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.957.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.732α = 90
b = 79.732β = 90
c = 321.975γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100DIFFRACTOMETERWEISSENBERG2002-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6B1.000Photon FactoryBL-6B

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25094.50.0640.06416.55321083034236.1
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)
2.22.280.2541.86

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1V4S2.242.3728759152994.660.22850.225880.27702RANDOM35.812
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]
1.680.841.68-2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.394
r_dihedral_angle_4_deg20.262
r_dihedral_angle_3_deg19.34
r_dihedral_angle_1_deg6.865
r_scangle_it5.673
r_scbond_it3.511
r_mcangle_it2.358
r_angle_refined_deg2.06
r_mcbond_it1.305
r_symmetry_vdw_refined0.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.394
r_dihedral_angle_4_deg20.262
r_dihedral_angle_3_deg19.34
r_dihedral_angle_1_deg6.865
r_scangle_it5.673
r_scbond_it3.511
r_mcangle_it2.358
r_angle_refined_deg2.06
r_mcbond_it1.305
r_symmetry_vdw_refined0.449
r_symmetry_hbond_refined0.369
r_nbtor_refined0.31
r_nbd_refined0.239
r_xyhbond_nbd_refined0.191
r_chiral_restr0.146
r_metal_ion_refined0.142
r_bond_refined_d0.024
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3505
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
WEISdata scaling
HKL-2000data reduction
HKL-2000data scaling