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Crystal structure of MKK7 (MAP2K7) covalently bound with CPT1-70-1
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, 0.25 M ammonium acetate,
0.1 M tris, pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.17 α = 90 b = 64.49 β = 90 c = 85.5 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 I03 0.97625 Diamond I03
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 2.05 30.385 99.1 0.098 0.107 0.041 0.998 10.7 6.6 20596
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 2.05 2.16 98.4 0.935 0.935 1.014 0.387 0.494 0.8 6.6
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 2.05 30.38 19531 1032 98.8 0.1908 0.1884 0.1955 0.2351 0.2437 RANDOM 44.495
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] -1.01 0.05 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.261 r_dihedral_angle_4_deg 14.705 r_dihedral_angle_3_deg 14.186 r_dihedral_angle_1_deg 5.976 r_angle_refined_deg 1.519 r_angle_other_deg 0.776 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 34.261 r_dihedral_angle_4_deg 14.705 r_dihedral_angle_3_deg 14.186 r_dihedral_angle_1_deg 5.976 r_angle_refined_deg 1.519 r_angle_other_deg 0.776 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 2107 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 70
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing