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Crystal structure of ERK2 with an allosteric inhibitor 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 10% PEG3350
0.1M HEPES pH 7.5
0.25M L-proline
glycerol
Crystal Properties Matthews coefficient Solvent content 2.78 55.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.653 α = 90 b = 82.653 β = 90 c = 275.074 γ = 90
Symmetry Space Group P 41 21 2
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 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.09 41.33 99.9 0.99 16.8 13.4 57640 51.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.16 99.6 0.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4QP1 2.09 41.33 1.33 57463 2873 99.62 0.2317 0.2296 0.2301 0.271 0.2712 66.72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.5162 f_angle_d 1.0091 f_chiral_restr 0.0526 f_plane_restr 0.0109 f_bond_d 0.0098
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5703 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 129
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing