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Crystal structure of MKK7 (MAP2K7) in complex with K00007
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 8.2 277.15 19% PEG3350, 0.1 M ammonium acetate,
0.1 M tris, pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.1 α = 90 b = 72.63 β = 90 c = 83.079 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 2014-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 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 2.3 36.06 99.6 0.066 0.075 0.034 0.998 11.2 4.6 15049
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 2.3 2.42 99.8 0.745 0.745 0.835 0.371 0.691 1 4.7
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 2.3 36.06 14263 749 99.39 0.2129 0.2106 0.2101 0.2549 0.2526 RANDOM 65.022
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] 1.22 -5.16 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.042 r_dihedral_angle_4_deg 19.601 r_dihedral_angle_3_deg 15.269 r_dihedral_angle_1_deg 7.386 r_angle_refined_deg 1.263 r_angle_other_deg 1.185 r_chiral_restr 0.055 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.042 r_dihedral_angle_4_deg 19.601 r_dihedral_angle_3_deg 15.269 r_dihedral_angle_1_deg 7.386 r_angle_refined_deg 1.263 r_angle_other_deg 1.185 r_chiral_restr 0.055 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 40
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing