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crystal structure of EGFR kinase domain in complex with Mitogen-inducible gene 6 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M Bis-Tris
0.2 M Ammonium acetate
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.459 α = 90 b = 81.865 β = 106.67 c = 96.19 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 DECTRIS PILATUS 6M 2014-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
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 2.7 50 96.5 0.11 9.1 2.8 23122
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 2.7 2.75 87.3 0.6 1.2 2.4
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 2RF9 2.7 50 20535 1099 89.82 0.18125 0.17854 0.1862 0.23197 0.2365 RANDOM 45.178
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] 0.01 0.06 -0.07 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.208 r_dihedral_angle_4_deg 21.005 r_dihedral_angle_3_deg 16.521 r_long_range_B_refined 8.504 r_long_range_B_other 8.491 r_dihedral_angle_1_deg 7.532 r_scangle_other 6.29 r_mcangle_it 5.323 r_mcangle_other 5.323 r_scbond_it 3.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.208 r_dihedral_angle_4_deg 21.005 r_dihedral_angle_3_deg 16.521 r_long_range_B_refined 8.504 r_long_range_B_other 8.491 r_dihedral_angle_1_deg 7.532 r_scangle_other 6.29 r_mcangle_it 5.323 r_mcangle_other 5.323 r_scbond_it 3.959 r_scbond_other 3.935 r_mcbond_it 3.391 r_mcbond_other 3.381 r_angle_refined_deg 1.173 r_angle_other_deg 0.694 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 5171 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing