6YZ4

Crystal structure of MKK7 (MAP2K7) with ibrutinib bound at allosteric site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DYL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8277.1516% PEG3350, 0.1 M tris pH 7.8, 0.25 M ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4950.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.51α = 90
b = 74.67β = 90
c = 87.17γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.02823DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.725.53599.90.0850.0920.0360.99913.16.539163
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7999.90.7810.7810.8490.3280.5522.36.5

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 REPLACEMENTTHROUGHOUT2dyl1.725.53537213189399.90.17110.16930.2061RANDOM28.894
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]
-0.01-0.090.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.198
r_dihedral_angle_4_deg20.43
r_dihedral_angle_3_deg13.565
r_dihedral_angle_1_deg6.03
r_angle_refined_deg1.61
r_angle_other_deg0.827
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.198
r_dihedral_angle_4_deg20.43
r_dihedral_angle_3_deg13.565
r_dihedral_angle_1_deg6.03
r_angle_refined_deg1.61
r_angle_other_deg0.827
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2295
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms85

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing