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Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric binding modes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277.15 19% PEG3350,
0.1 M ammonium acetate,
0.1 M tris, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.47 50.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.111 α = 90 b = 74.955 β = 90 c = 86.666 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.02823 Diamond I04
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 19.55 99.9 0.106 0.115 0.042 0.997 12.1 7.3 24057
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) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.901 0.901 0.968 0.351 0.901 0.8 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2dyl 2 19.55 22831 1176 99.84 0.1815 0.1789 0.186 0.2304 0.2329 RANDOM 38.529
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.721 r_dihedral_angle_4_deg 18.32 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_1_deg 5.959 r_angle_refined_deg 1.491 r_angle_other_deg 0.762 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.721 r_dihedral_angle_4_deg 18.32 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_1_deg 5.959 r_angle_refined_deg 1.491 r_angle_other_deg 0.762 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2290 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing