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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERK pdb entry 1ERK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277.15 25% 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 coefficient Solvent content 3.1 60.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.729 α = 90 b = 96.729 β = 90 c = 95.382 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M Kirkpatrick Baez bimorph mirror pair 2014-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 21.57 98.2 0.064 15.3 7.1 81004 81001 17.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 96.9 0.652 3 7.1 11574
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1ERK 1.5 83.77 2 81001 77002 3995 97.91 0.14667 0.1456 0.1459 0.16709 0.167 RANDOM 33.32
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] 0.33 0.17 0.33 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.766 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 11.96 r_long_range_B_other 7.74 r_long_range_B_refined 7.738 r_dihedral_angle_1_deg 5.967 r_scangle_other 2.886 r_scbond_it 2.177 r_scbond_other 2.176 r_angle_refined_deg 1.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.766 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 11.96 r_long_range_B_other 7.74 r_long_range_B_refined 7.738 r_dihedral_angle_1_deg 5.967 r_scangle_other 2.886 r_scbond_it 2.177 r_scbond_other 2.176 r_angle_refined_deg 1.617 r_mcangle_it 1.562 r_mcangle_other 1.562 r_mcbond_it 1.037 r_mcbond_other 1.036 r_angle_other_deg 0.823 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2846 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 149
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling