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X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a complex with ligand and MgATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Iodine substructure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 288 PEG8K, Ammonium phosphate, Imidazole-malate, DTT, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.27 62.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.591 α = 90 b = 81.591 β = 90 c = 129.213 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2001-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 48 0.052 31 6.5 18590 18389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 0.74 0.32 1.8
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 Iodine-SAD THROUGHOUT Iodine substructure 2.4 47.7 17466 923 96.45 0.24577 0.24458 0.245 0.26933 0.2712 RANDOM 20.815
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] 1.92 0.96 1.92 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.981 r_scangle_it 1.823 r_scbond_it 0.997 r_angle_refined_deg 0.966 r_mcangle_it 0.862 r_angle_other_deg 0.715 r_mcbond_it 0.468 r_nbd_other 0.186 r_symmetry_vdw_other 0.176 r_nbd_refined 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.981 r_scangle_it 1.823 r_scbond_it 0.997 r_angle_refined_deg 0.966 r_mcangle_it 0.862 r_angle_other_deg 0.715 r_mcbond_it 0.468 r_nbd_other 0.186 r_symmetry_vdw_other 0.176 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.105 r_symmetry_hbond_refined 0.098 r_nbtor_other 0.08 r_chiral_restr 0.054 r_metal_ion_refined 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2261 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 data scaling CNX phasing