4NO7

Human Glucokinase in complex with a nanomolar 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 DROP7.529330% PEG 4000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.3α = 90
b = 81.3β = 90
c = 85.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2008-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0001SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.719.74100503334781523
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)RedundancyNumber Unique Reflections (All)
11.71.7988.60.770.771.52.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1V4S1.719.7432503334781525171000.191250.189590.2226RANDOM24.436
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]
0.80.18-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.509
r_dihedral_angle_4_deg19.841
r_dihedral_angle_3_deg15.862
r_dihedral_angle_1_deg5.5
r_scangle_it3.618
r_scbond_it2.228
r_angle_refined_deg1.787
r_mcangle_it1.445
r_mcbond_it0.899
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.509
r_dihedral_angle_4_deg19.841
r_dihedral_angle_3_deg15.862
r_dihedral_angle_1_deg5.5
r_scangle_it3.618
r_scbond_it2.228
r_angle_refined_deg1.787
r_mcangle_it1.445
r_mcbond_it0.899
r_nbtor_refined0.31
r_symmetry_vdw_refined0.233
r_nbd_refined0.213
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.152
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3502
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing