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Phosphorylated ERK2 with Vertex-11e
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ERK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 16.5% PEG3350,100 mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.986 α = 90 b = 78.139 β = 90 c = 152.601 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 DECTRIS PILATUS3 S 6M 2015-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 2.47 30 100 0.098 9.5 6.1 19482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.54 99.9 0.93 1.054 0.49 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ERK 2.54 30 16372 896 99.9 0.19562 0.19303 0.1972 0.24081 0.2357 RANDOM 73.051
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 21.327 r_dihedral_angle_3_deg 16.743 r_long_range_B_other 11.264 r_long_range_B_refined 11.217 r_scangle_other 9.13 r_mcangle_it 8.33 r_mcangle_other 8.329 r_dihedral_angle_1_deg 7.163 r_scbond_other 6.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 21.327 r_dihedral_angle_3_deg 16.743 r_long_range_B_other 11.264 r_long_range_B_refined 11.217 r_scangle_other 9.13 r_mcangle_it 8.33 r_mcangle_other 8.329 r_dihedral_angle_1_deg 7.163 r_scbond_other 6.595 r_scbond_it 6.577 r_mcbond_it 6.005 r_mcbond_other 5.997 r_angle_refined_deg 1.657 r_angle_other_deg 1.187 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 2839 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing