3DY7

X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a complex with ligand and MgATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S9JPDB ENTRY 1S9J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5288PEG8K, Ammonium phosphate, Imidazole-malate, DTT, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
3.2862.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.754α = 90
b = 81.754β = 90
c = 128.893γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210single crystal2001-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.73093.40.0520.0525.97125271252780.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.895.60.4130.41365.91260

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1S9J2.7301189563293.230.248340.247280.26898RANDOM69.209
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]
2.591.32.59-3.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.711
r_dihedral_angle_3_deg21.377
r_dihedral_angle_4_deg20.828
r_dihedral_angle_1_deg5.398
r_scangle_it2.258
r_angle_refined_deg1.29
r_scbond_it1.264
r_mcangle_it1.063
r_mcbond_it0.563
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.711
r_dihedral_angle_3_deg21.377
r_dihedral_angle_4_deg20.828
r_dihedral_angle_1_deg5.398
r_scangle_it2.258
r_angle_refined_deg1.29
r_scbond_it1.264
r_mcangle_it1.063
r_mcbond_it0.563
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2037
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling