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Crystal structure of ERK2 covalently bound to SM1-71
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 277.15 0.9M Li2SO4 and 0.1M citrate 5.9
Crystal Properties Matthews coefficient Solvent content 2.91 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.751 α = 90 b = 91.751 β = 90 c = 99.305 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 DECTRIS EIGER X 16M 2018-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.05 49.65 100 0.057 0.999 16.1 7.9 30813 38.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 100 0.911 0.783 2 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4QTA 2.05 49.65 29380 1400 99.96 0.18507 0.18322 0.22096 0.2288 RANDOM 55.794
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] -0.04 -0.02 -0.04 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.277 r_dihedral_angle_4_deg 21.555 r_dihedral_angle_3_deg 14.461 r_long_range_B_other 7.1 r_long_range_B_refined 7.098 r_dihedral_angle_1_deg 6.311 r_scangle_other 3.461 r_mcangle_it 2.631 r_mcangle_other 2.631 r_scbond_it 2.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.277 r_dihedral_angle_4_deg 21.555 r_dihedral_angle_3_deg 14.461 r_long_range_B_other 7.1 r_long_range_B_refined 7.098 r_dihedral_angle_1_deg 6.311 r_scangle_other 3.461 r_mcangle_it 2.631 r_mcangle_other 2.631 r_scbond_it 2.159 r_scbond_other 2.149 r_mcbond_it 1.677 r_mcbond_other 1.676 r_angle_refined_deg 1.348 r_angle_other_deg 0.734 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2834 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing