3O08

Crystal structure of dimeric KlHxk1 in crystal form I


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IG8PDB entry 1IG8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.42921MICROL RESERVOIR + 1MICROL PROTEIN; RESERVOIR: 2.5M AMMONIA SULFATE, 0.1M CHES PH 9.4, 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
2.3748.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.692α = 90
b = 113.219β = 90
c = 91.234γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateSi, coated with 200 layers of Mo/Si2005-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.8940BESSY14.3

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
123099.80.07226.26975969639-331.3
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)
22.0598.90.5054.96.25044

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 1IG8229.9768555103399.870.185870.185010.24366RANDOM31.672
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]
0.071.58-1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.912
r_dihedral_angle_4_deg23.938
r_dihedral_angle_3_deg16.828
r_scangle_it6.974
r_dihedral_angle_1_deg6.493
r_scbond_it5.2
r_mcangle_it3.109
r_mcbond_it2.333
r_angle_refined_deg2.017
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.912
r_dihedral_angle_4_deg23.938
r_dihedral_angle_3_deg16.828
r_scangle_it6.974
r_dihedral_angle_1_deg6.493
r_scbond_it5.2
r_mcangle_it3.109
r_mcbond_it2.333
r_angle_refined_deg2.017
r_chiral_restr0.146
r_bond_refined_d0.024
r_gen_planes_refined0.011
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 Atoms7391
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms123

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling