8X34 | pdb_00008x34

Human Kelch like-ECH Associated Protein 1 (Keap1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U6D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52774.0 M Ammonium acetate, 0.1 M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
575.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.644α = 90
b = 75.825β = 90
c = 218.656γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELRIGAKU HyPix-30002023-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU PhotonJet-R1.54

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
1331.1599.760.012.071025899
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)
13.013.0297.90.992

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT331.1523737216299.620.27540.27540.280.32910.28RANDOM58.83
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]
-0.09-0.010.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.146
r_long_range_B_refined14.247
r_mcangle_it8.617
r_dihedral_angle_1_deg7.41
r_mcbond_it5.117
r_dihedral_angle_2_deg5.037
r_scbond_it5.015
r_angle_refined_deg1.363
r_chiral_restr0.106
r_bond_refined_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4362
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing