6YG2

Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric binding modes


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8277.1519% PEG3350, 0.1 M ammonium acetate, 0.1 M tris, pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.4750.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.111α = 90
b = 74.955β = 90
c = 86.666γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-10-13MSINGLE 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
1219.5599.90.1060.1150.0420.99712.17.324057
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)
122.111000.9010.9010.9680.3510.9010.87.4

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 REPLACEMENTTHROUGHOUT2dyl219.5522831117699.840.18150.17890.2304RANDOM38.529
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]
0.37-0.06-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.721
r_dihedral_angle_4_deg18.32
r_dihedral_angle_3_deg13.806
r_dihedral_angle_1_deg5.959
r_angle_refined_deg1.491
r_angle_other_deg0.762
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.721
r_dihedral_angle_4_deg18.32
r_dihedral_angle_3_deg13.806
r_dihedral_angle_1_deg5.959
r_angle_refined_deg1.491
r_angle_other_deg0.762
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2290
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing