3I5Z

Crystal structure of ERK2 bound to (S)-N-(2-hydroxy-1-phenylethyl)-4-(5-methyl-2-(phenylamino)pyrimidin-4-yl)-1H-pyrrole-2-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house unpublished structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2298Protein: 14 mg/ml, 20 mM Tris-HCl pH 7.0, 5 mM DTT, 200 mM NaCl. Precipitant: 100 mM HEPES pH 7.2, 28-30% PEG MME 2000, 200 mM Ammonium sulfate, 20 mM 2-Mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.948α = 90
b = 70.751β = 90
c = 118.46γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISYale mirrors2001-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.29195.20.07312.318555
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)
12.22.2675.40.3011185

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X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTin-house unpublished structure2.260.74181121424930.2170.2140.258RANDOM20.622
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]
-0.52-1.041.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.888
r_dihedral_angle_4_deg16.931
r_dihedral_angle_3_deg16.754
r_dihedral_angle_1_deg5.071
r_scangle_it1.975
r_scbond_it1.205
r_angle_refined_deg1.156
r_mcangle_it0.843
r_mcbond_it0.448
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.888
r_dihedral_angle_4_deg16.931
r_dihedral_angle_3_deg16.754
r_dihedral_angle_1_deg5.071
r_scangle_it1.975
r_scbond_it1.205
r_angle_refined_deg1.156
r_mcangle_it0.843
r_mcbond_it0.448
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2694
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms51

Software

Software
Software NamePurpose
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing