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Structure of human ERK2 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket
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 7.5 277.15 30% PEG4000 and 0.2 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.82 α = 90 b = 75.54 β = 90 c = 103.59 γ = 90
Symmetry Space Group P 21 21 21
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 2013-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97960 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 1.45 33 99.9 0.09 12.5 7.9 60441 60366 11.9
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 1.45 1.53 99.7 0.71 2.6 7.5 8701
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 1.45 61.04 2 60366 57320 3046 99.93 0.16008 0.15839 0.1587 0.19147 0.1912 RANDOM 21.194
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] -0.69 0.09 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.044 r_dihedral_angle_4_deg 18.069 r_dihedral_angle_3_deg 11.93 r_long_range_B_other 6.889 r_long_range_B_refined 6.887 r_dihedral_angle_1_deg 5.318 r_scangle_other 2.745 r_scbond_it 1.8 r_scbond_other 1.8 r_angle_refined_deg 1.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.044 r_dihedral_angle_4_deg 18.069 r_dihedral_angle_3_deg 11.93 r_long_range_B_other 6.889 r_long_range_B_refined 6.887 r_dihedral_angle_1_deg 5.318 r_scangle_other 2.745 r_scbond_it 1.8 r_scbond_other 1.8 r_angle_refined_deg 1.698 r_mcangle_it 1.592 r_mcangle_other 1.592 r_mcbond_it 0.994 r_mcbond_other 0.993 r_angle_other_deg 0.853 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2715 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 86
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling