4AN2

Crystal structures of human MEK1 with carboxamide-based allosteric inhibitor XL518 (GDC-0973), or related analogs.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN HOUSE MEK1-AMPPCP STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.9MEK1 (8 MG/ML) WAS INCUBATED WITH INHIBITOR (300 MICROMOLAR FINAL CONCENTRATION) AND AMPPCP (2.8 MM FINAL CONCENTRATION) FOR TWO HOURS ON ICE, FOLLOWED BY CRYSTALLIZION VS. 26.5% PEG-2000 MME, 0.1 M TRIMETHYLAMINE N- OXIDE AND 0.1 M TRIS (PH 8.9)
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.844α = 90
b = 108.844β = 90
c = 47.71γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2005-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.554.3999.80.0715.24.4128192
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6899.90.562.34.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN HOUSE MEK1-AMPPCP STRUCTURE2.594.071078357899.890.214930.210790.29898RANDOM53.06
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]
-0.5-0.25-0.50.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.722
r_dihedral_angle_4_deg22.051
r_dihedral_angle_3_deg19.513
r_dihedral_angle_1_deg7.279
r_scangle_it4.229
r_scbond_it2.828
r_angle_refined_deg2.178
r_mcangle_it1.802
r_mcbond_it1.016
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.722
r_dihedral_angle_4_deg22.051
r_dihedral_angle_3_deg19.513
r_dihedral_angle_1_deg7.279
r_scangle_it4.229
r_scbond_it2.828
r_angle_refined_deg2.178
r_mcangle_it1.802
r_mcbond_it1.016
r_nbtor_refined0.322
r_symmetry_vdw_refined0.278
r_nbd_refined0.26
r_xyhbond_nbd_refined0.197
r_symmetry_hbond_refined0.14
r_chiral_restr0.139
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_metal_ion_refined0.006
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 AtomsNumber
Protein Atoms2209
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing