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Crystal structure of human MEK2 in complex with Refametinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9I Dual specificity mitogen-activated protein kinase kinase 2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 295 0.2M Sodium Phosphate dibasic dehydrate, 20% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.18 61.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.346 α = 90 b = 261.666 β = 90 c = 75.374 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 315r 2021-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9795 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 3.3 49.4 98.44 0.143 0.055 0.991 13.2 6.8 44524 61.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.36 0.729 0.867 2.64
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.3 49.4 1.35 44524 2000 98.44 0.2096 0.2081 0.2102 0.2425 0.2443 56.24
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 13.9783 f_angle_d 0.6896 f_chiral_restr 0.0423 f_plane_restr 0.0051 f_bond_d 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14440 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 378
Software Software Software Name Purpose PHENIX refinement DENZO data reduction HKL-2000 data scaling PHASER phasing