5FNU

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
2.6152.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.297α = 90
b = 103.297β = 90
c = 56.434γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU CCD2013-04-30MSINGLE 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
11.7851.6587.50.0418.72.228698
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)
11.781.8444.10.193.5

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 1X2J1.7851.6527225147387.50.168070.166080.20487RANDOM21.563
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]
-0.09-0.05-0.090.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.85
r_dihedral_angle_4_deg16.767
r_dihedral_angle_3_deg14.072
r_dihedral_angle_1_deg7.164
r_scbond_it1.803
r_angle_refined_deg1.439
r_mcbond_it0.781
r_angle_other_deg0.17
r_chiral_restr0.101
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.85
r_dihedral_angle_4_deg16.767
r_dihedral_angle_3_deg14.072
r_dihedral_angle_1_deg7.164
r_scbond_it1.803
r_angle_refined_deg1.439
r_mcbond_it0.781
r_angle_other_deg0.17
r_chiral_restr0.101
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 Atoms2215
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling