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Structure of human ERK1 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 2ZOQ pdb entry 2ZOQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277.15 33% PEG4000, 0.1 M Tris pH 8.0 and 0.2 M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.98 α = 90 b = 94.01 β = 91.71 c = 65.36 γ = 90
Symmetry Space Group P 1 21 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 2013-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.91997 Diamond I03
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 1.4 38.15 95.8 0.089 8.8 4.1 140419 140385 9.8
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 1.4 1.48 93.3 0.618 2.2 3.9 19971
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2ZOQ 1.4 32.74 2 140385 133341 7044 95.55 0.14846 0.14704 0.17505 0.1813 RANDOM 16.182
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] -0.86 -0.07 1.25 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.14 r_dihedral_angle_4_deg 18.793 r_dihedral_angle_3_deg 11.41 r_long_range_B_refined 6.252 r_long_range_B_other 6.252 r_dihedral_angle_1_deg 5.695 r_scangle_other 2.78 r_scbond_it 1.812 r_scbond_other 1.812 r_angle_refined_deg 1.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.14 r_dihedral_angle_4_deg 18.793 r_dihedral_angle_3_deg 11.41 r_long_range_B_refined 6.252 r_long_range_B_other 6.252 r_dihedral_angle_1_deg 5.695 r_scangle_other 2.78 r_scbond_it 1.812 r_scbond_other 1.812 r_angle_refined_deg 1.631 r_mcangle_it 1.555 r_mcangle_other 1.555 r_mcbond_it 0.987 r_mcbond_other 0.973 r_angle_other_deg 0.789 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5692 Nucleic Acid Atoms Solvent Atoms 1111 Heterogen Atoms 193
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling