3I60

Crystal structure of ERK2 bound to (S)-4-(2-(2-chlorophenylamino)-5-methylpyrimidin-4-yl)-N-(2-hydroxy-1-phenylethyl)-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otherin-house unpublished structure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
2.1242.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.061α = 90
b = 70.251β = 90
c = 119.598γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISYale mirrors2001-11-15MSINGLE 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
12.55595.50.05619.312882
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)
12.52.57920.3291002

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X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTin-house unpublished structure2.55512498101492.980.2110.2070.248RANDOM23.63
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]
0.12-0.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.633
r_dihedral_angle_4_deg18.296
r_dihedral_angle_3_deg14.889
r_dihedral_angle_1_deg5.172
r_scangle_it2.19
r_scbond_it1.277
r_angle_refined_deg1.053
r_mcangle_it1.033
r_mcbond_it0.547
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.633
r_dihedral_angle_4_deg18.296
r_dihedral_angle_3_deg14.889
r_dihedral_angle_1_deg5.172
r_scangle_it2.19
r_scbond_it1.277
r_angle_refined_deg1.053
r_mcangle_it1.033
r_mcbond_it0.547
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2732
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms47

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CNSphasing