8IN0 | pdb_00008in0

Structure of the Keap1 Kelch domain in complex with PGAM5-derived peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298Ammonium sulfate, Lithium sulfate, Sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.1943.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.655α = 90
b = 103.655β = 90
c = 56.167γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.8

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.824.70499.910.95714.685.831965
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8640.605

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONAB INITIO PHASINGFREE R-VALUE1.824.70431240153697.4850.2550.25330.260.28470.2917.466
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]
0.0040.0020.004-0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.322
r_dihedral_angle_4_deg17.635
r_dihedral_angle_3_deg14.244
r_dihedral_angle_1_deg8.506
r_lrange_it6.127
r_lrange_other5.862
r_scangle_it3.405
r_scangle_other3.288
r_mcangle_other2.614
r_mcangle_it2.613
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2304
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing