5FNT

Structure of the Keap1 Kelch domain in complex with a small molecule inhibitor.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X2JPDB ENTRY 1X2J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.3-0.6 (NH4)2SO4, 0.4-1.4 M LI2SO4 AND 0.1 M NA3CITRATE-HCL PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.652.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.349α = 90
b = 103.349β = 90
c = 56.36γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU CCD2012-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+

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
11.7989.590.60.0610.3229094
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)
11.791.8351.70.182.6

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 1X2J1.7990.627616147890.60.1720.170370.20219RANDOM20.696
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]
-0.29-0.14-0.290.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.802
r_dihedral_angle_4_deg17.795
r_dihedral_angle_3_deg13.044
r_dihedral_angle_1_deg7.336
r_scbond_it1.589
r_angle_refined_deg1.467
r_mcbond_it0.789
r_angle_other_deg0.204
r_chiral_restr0.103
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.802
r_dihedral_angle_4_deg17.795
r_dihedral_angle_3_deg13.044
r_dihedral_angle_1_deg7.336
r_scbond_it1.589
r_angle_refined_deg1.467
r_mcbond_it0.789
r_angle_other_deg0.204
r_chiral_restr0.103
r_bond_refined_d0.011
r_bond_other_d0.002
r_gen_planes_refined0.001
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_mcangle_it
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2219
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling