3O5B

Crystal structure of dimeric KlHxk1 in crystal form VII with glucose bound (open state)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O08PDB entry 3O08

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92921microL reservoir + 1microL protein, reservoir: 18% PEG6000, 0.9M LiCl, 2mM MgCl2, 0.1M Bicine pH 9.0, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.5852.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.14α = 90
b = 122.2β = 90
c = 92.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELBent, vertically focussing2009-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8148EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.973099.60.03528.44.27907778731-338.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.972.0299.20.4922.8745724

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3O081.9729.977579115399.60.205110.204370.25506RANDOM40.129
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]
-0.953.38-2.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg20.401
r_dihedral_angle_3_deg17.82
r_scangle_it8.654
r_scbond_it6.629
r_dihedral_angle_1_deg5.986
r_mcangle_it3.896
r_mcbond_it2.837
r_angle_refined_deg1.709
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg20.401
r_dihedral_angle_3_deg17.82
r_scangle_it8.654
r_scbond_it6.629
r_dihedral_angle_1_deg5.986
r_mcangle_it3.896
r_mcbond_it2.837
r_angle_refined_deg1.709
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7443
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms39

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling