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Crystal structure of MKK7 (MAP2K7) covalently bound with type-II inhibitor TL10-105
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 8.2 293.15 19% PEG3350, 0.15 M ammonium acetate,
0.1 M tris, pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.651 α = 90 b = 69.934 β = 119.36 c = 73.763 γ = 90
Symmetry Space Group P 1 21 1
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 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 2.15 47.33 99.9 0.101 0.113 0.05 0.996 10 5.3 35192
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 2.15 2.27 99.9 0.906 0.906 1.02 0.46 0.659 0.7 5.1
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 2.15 47.33 33542 1630 99.92 0.2053 0.2036 0.2056 0.2389 0.2437 RANDOM 62.631
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] 3.82 3.1 -4.17 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.051 r_dihedral_angle_4_deg 17.549 r_dihedral_angle_3_deg 15.622 r_dihedral_angle_1_deg 6.658 r_angle_refined_deg 1.336 r_angle_other_deg 1.016 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.051 r_dihedral_angle_4_deg 17.549 r_dihedral_angle_3_deg 15.622 r_dihedral_angle_1_deg 6.658 r_angle_refined_deg 1.336 r_angle_other_deg 1.016 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4514 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 108
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing