5FZJ

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 M (NH4)2SO4, 0.4-1.4 M LI2SO4, 0.1 M NA3CITRATE-HCL PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.652.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.483α = 90
b = 103.483β = 90
c = 56.094γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU CCD2011-08-03MSINGLE 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
12.012994.60.0413.52.121811
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)
12.012.0484.30.24

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 1X2J2.012920708110494.60.169470.167090.21401RANDOM28.683
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]
-0.86-0.43-0.862.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.048
r_dihedral_angle_4_deg18.549
r_dihedral_angle_3_deg13.248
r_dihedral_angle_1_deg7.557
r_scbond_it2.26
r_angle_refined_deg1.483
r_mcbond_it1.153
r_mcbond_other1.153
r_angle_other_deg0.909
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.048
r_dihedral_angle_4_deg18.549
r_dihedral_angle_3_deg13.248
r_dihedral_angle_1_deg7.557
r_scbond_it2.26
r_angle_refined_deg1.483
r_mcbond_it1.153
r_mcbond_other1.153
r_angle_other_deg0.909
r_chiral_restr0.087
r_bond_refined_d0.01
r_bond_other_d0.002
r_gen_planes_refined
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_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 Atoms266
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling