1S9J

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
otherIodine substructure

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
3.2762.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.591α = 90
b = 81.591β = 90
c = 129.213γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

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
12.4480.052316.51859018389
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)
12.42.460.740.321.8

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 DIFFRACTIONIodine-SADTHROUGHOUTIodine substructure2.447.71746692396.450.245770.244580.26933RANDOM20.815
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]
1.920.961.92-2.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.981
r_scangle_it1.823
r_scbond_it0.997
r_angle_refined_deg0.966
r_mcangle_it0.862
r_angle_other_deg0.715
r_mcbond_it0.468
r_nbd_other0.186
r_symmetry_vdw_other0.176
r_nbd_refined0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.981
r_scangle_it1.823
r_scbond_it0.997
r_angle_refined_deg0.966
r_mcangle_it0.862
r_angle_other_deg0.715
r_mcbond_it0.468
r_nbd_other0.186
r_symmetry_vdw_other0.176
r_nbd_refined0.161
r_symmetry_vdw_refined0.14
r_xyhbond_nbd_refined0.105
r_symmetry_hbond_refined0.098
r_nbtor_other0.08
r_chiral_restr0.054
r_metal_ion_refined0.053
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2261
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4data scaling
CNXphasing