3O1W

Crystal structure of dimeric KlHxk1 in crystal form III


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.62921MICROL RESERVOIR + 1MICROL PROTEIN, RESERVOIR: 2.2 M AMMONIA DIHYDROGEN PHOSPHATE, 0.1M CHES PH 9.6, 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
2.7755.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.311α = 90
b = 135.844β = 92.06
c = 72.591γ = 90
Symmetry
Space GroupP 1 21 1

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
11.663094.50.05235.3129723-333.4
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)
1.661.795.30.4852.25.18687

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 3O081.6629.85128367131394.450.161720.161330.20139RANDOM22.928
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]
0.8-0.89-0.3-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.711
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg13.634
r_dihedral_angle_1_deg5.812
r_scangle_it5.064
r_scbond_it3.177
r_angle_refined_deg2.141
r_mcangle_it1.892
r_mcbond_it1.213
r_chiral_restr0.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.711
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg13.634
r_dihedral_angle_1_deg5.812
r_scangle_it5.064
r_scbond_it3.177
r_angle_refined_deg2.141
r_mcangle_it1.892
r_mcbond_it1.213
r_chiral_restr0.157
r_bond_refined_d0.026
r_gen_planes_refined0.013
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 Atoms7526
Nucleic Acid Atoms
Solvent Atoms743
Heterogen Atoms100

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling