1U6D

Crystal structure of the Kelch domain of human Keap1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52774% PEG 4000, 100 mM Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.652.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.892α = 90
b = 85.892β = 90
c = 148.753γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2004-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8510099.90.08133.914.42816928169
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)
1.851.921000.524.22749

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRTHROUGHOUT1.8519.882452313161000.149410.147660.18237RANDOM17.003
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]
-0.57-0.29-0.570.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.277
r_scangle_it2.78
r_scbond_it1.7
r_angle_refined_deg1.257
r_mcangle_it1.051
r_angle_other_deg0.805
r_mcbond_it0.56
r_symmetry_vdw_other0.295
r_nbd_other0.251
r_nbd_refined0.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.277
r_scangle_it2.78
r_scbond_it1.7
r_angle_refined_deg1.257
r_mcangle_it1.051
r_angle_other_deg0.805
r_mcbond_it0.56
r_symmetry_vdw_other0.295
r_nbd_other0.251
r_nbd_refined0.185
r_symmetry_vdw_refined0.133
r_symmetry_hbond_refined0.127
r_xyhbond_nbd_refined0.116
r_chiral_restr0.088
r_nbtor_other0.077
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
SOLVEphasing