4QTE

Structure of ERK2 in complex with VTX-11e, 4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYLPYRIMIDIN-4-YL}-N-[(1S)-1-(3-CHLOROPHENYL)-2-HYDROXYETHYL]-1H-PYRROLE-2-CARBOXAMIDE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ERKpdb entry 1ERK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5277.1525% PEG smears (PEG2000, PEG3350, PEG4000 and PEG5000MME), 0.1 M cacodylate pH 5.5 and 0.2 M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
3.160.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.729α = 90
b = 96.729β = 90
c = 95.382γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MKirkpatrick Baez bimorph mirror pair2014-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
11.521.5798.20.06415.37.1810048100117.9
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)
11.51.5896.90.65237.111574

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1ERK1.583.7728100177002399597.910.146670.14560.16709RANDOM33.32
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]
0.330.170.33-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.766
r_dihedral_angle_4_deg17.655
r_dihedral_angle_3_deg11.96
r_long_range_B_other7.74
r_long_range_B_refined7.738
r_dihedral_angle_1_deg5.967
r_scangle_other2.886
r_scbond_it2.177
r_scbond_other2.176
r_angle_refined_deg1.617
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.766
r_dihedral_angle_4_deg17.655
r_dihedral_angle_3_deg11.96
r_long_range_B_other7.74
r_long_range_B_refined7.738
r_dihedral_angle_1_deg5.967
r_scangle_other2.886
r_scbond_it2.177
r_scbond_other2.176
r_angle_refined_deg1.617
r_mcangle_it1.562
r_mcangle_other1.562
r_mcbond_it1.037
r_mcbond_other1.036
r_angle_other_deg0.823
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2846
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms149

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling