4AN3

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
otherUNPUBLISHED MEK1-ATP STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.9SITTING 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 coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.659α = 90
b = 108.659β = 90
c = 50.113γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDMIRRORS2005-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
12.144.2399.50.078.13.2199012
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)
12.12.181000.462.23.2

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 REPLACEMENTTHROUGHOUTUNPUBLISHED MEK1-ATP STRUCTURE2.144.2218755102199.370.228650.225740.28311RANDOM44.537
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]
-1.99-0.99-1.992.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.931
r_dihedral_angle_4_deg18.065
r_dihedral_angle_3_deg17.791
r_dihedral_angle_1_deg7.106
r_scangle_it4.385
r_scbond_it3.035
r_angle_refined_deg2.1
r_mcangle_it1.861
r_mcbond_it1.105
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.931
r_dihedral_angle_4_deg18.065
r_dihedral_angle_3_deg17.791
r_dihedral_angle_1_deg7.106
r_scangle_it4.385
r_scbond_it3.035
r_angle_refined_deg2.1
r_mcangle_it1.861
r_mcbond_it1.105
r_nbtor_refined0.315
r_symmetry_vdw_refined0.264
r_nbd_refined0.249
r_xyhbond_nbd_refined0.209
r_symmetry_hbond_refined0.191
r_chiral_restr0.13
r_metal_ion_refined0.038
r_bond_refined_d0.02
r_gen_planes_refined0.008
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 AtomsNumber
Protein Atoms2191
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing