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Crystal structures of human MEK1 with carboxamide-based allosteric inhibitor XL518 (GDC-0973), or related analogs.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other UNPUBLISHED MEK1-ATP STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 SITTING DROP VAPOR DIFFUSION VS. 26.5 % PEG-2000 MME, 0.1 M TRIMETHYLAMINE N-OXIDE, 0.1 M TRIS (PH 8.9)
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.659 α = 90 b = 108.659 β = 90 c = 50.113 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 MARMOSAIC 325 mm CCD MIRRORS 2005-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.1 44.23 99.5 0.07 8.1 3.2 19901 2
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 2.1 2.18 100 0.46 2.2 3.2
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT UNPUBLISHED MEK1-ATP STRUCTURE 2.1 44.22 18755 1021 99.37 0.22865 0.22574 0.2256 0.28311 0.2844 RANDOM 44.537
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] -1.99 -0.99 -1.99 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.931 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_1_deg 7.106 r_scangle_it 4.385 r_scbond_it 3.035 r_angle_refined_deg 2.1 r_mcangle_it 1.861 r_mcbond_it 1.105 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.931 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_1_deg 7.106 r_scangle_it 4.385 r_scbond_it 3.035 r_angle_refined_deg 2.1 r_mcangle_it 1.861 r_mcbond_it 1.105 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.249 r_xyhbond_nbd_refined 0.209 r_symmetry_hbond_refined 0.191 r_chiral_restr 0.13 r_metal_ion_refined 0.038 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2191 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing