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Crystal structure of MKK7 (MAP2K7) in an active state, allosterically triggered by the N-terminal helix
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 7.5 277.15 27% PEG3350, 0.2 M potassium thiocyanate, 10% ethylene glycol, 0.1 M bis-tris propane, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.16 α = 90 b = 67.87 β = 114.76 c = 142.78 γ = 90
Symmetry Space Group C 1 2 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 2015-10-09 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 2.22 64.83 99.8 0.09 0.105 0.053 0.996 8.2 3.7 54756
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 2.22 2.34 99.8 0.661 0.661 0.779 0.406 0.675 1.1 3.5
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 2.22 64.83 52028 2724 99.75 0.2051 0.2037 0.2084 0.2317 0.2347 RANDOM 63.77
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] -1.56 -0.91 2.88 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.24 r_dihedral_angle_4_deg 20.258 r_dihedral_angle_3_deg 14.536 r_dihedral_angle_1_deg 5.998 r_angle_refined_deg 1.407 r_angle_other_deg 1.183 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.24 r_dihedral_angle_4_deg 20.258 r_dihedral_angle_3_deg 14.536 r_dihedral_angle_1_deg 5.998 r_angle_refined_deg 1.407 r_angle_other_deg 1.183 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7318 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 96
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing