2DYH

Crystal structure of the Keap1 protein in complexed with the N-terminal region of the Nrf2 transcription factor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6298Ammonium sulfate, Lithium Sulfate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.131α = 90
b = 103.131β = 90
c = 56.141γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATERIGAKU RAXIS IV++mirrors2005-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.95098.20.0868.62704326542-3
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)
1.91.97880.3983.62359

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 1X2J1.92025143133598.20.174320.172370.21102RANDOM34.302
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]
-0.8-0.4-0.81.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.524
r_dihedral_angle_4_deg19.811
r_dihedral_angle_3_deg13.53
r_dihedral_angle_1_deg7.018
r_scangle_it3.81
r_scbond_it2.691
r_mcangle_it1.808
r_angle_refined_deg1.55
r_mcbond_it1.142
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.524
r_dihedral_angle_4_deg19.811
r_dihedral_angle_3_deg13.53
r_dihedral_angle_1_deg7.018
r_scangle_it3.81
r_scbond_it2.691
r_mcangle_it1.808
r_angle_refined_deg1.55
r_mcbond_it1.142
r_nbtor_refined0.304
r_nbd_refined0.221
r_symmetry_vdw_refined0.218
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.149
r_chiral_restr0.118
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2321
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing