3O8M

Crystal structure of monomeric KlHxk1 in crystal form XI with glucose bound (closed 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 DROP72920.2microL reservoir + 0.2microL protein, reservoir: 20% PEG6000, 1M LiCl, 0.1M Hepes pH 7.0, protein: 6.6mg/ml KlHxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 10mM AMPPNP, 10mM Glucose, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.3647.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.575α = 90
b = 75.599β = 90
c = 103.857γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD1st mirror: Silicon, active surface 50 nm Rh-coated, 2nd mirror: Glas, active surface 50 nm Rh-coated2008-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.423096.20.0522.67.19654792838-323.1
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)
1.421.4672.70.4912.94.15134

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 3O081.4229.791406136796.190.186940.186510.21578RANDOM18.898
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]
-0.35-0.991.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.218
r_dihedral_angle_4_deg16.89
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg6.565
r_scangle_it4.365
r_scbond_it3.257
r_angle_refined_deg2.313
r_mcangle_it2.224
r_mcbond_it1.679
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.218
r_dihedral_angle_4_deg16.89
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg6.565
r_scangle_it4.365
r_scbond_it3.257
r_angle_refined_deg2.313
r_mcangle_it2.224
r_mcbond_it1.679
r_chiral_restr0.163
r_bond_refined_d0.028
r_gen_planes_refined0.015
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 Atoms3669
Nucleic Acid Atoms
Solvent Atoms611
Heterogen Atoms28

Software

Software
Software NamePurpose
MAR345data collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling