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Crystal structure of EGFR kinase domain T790M mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ITN PDB ENTRY 2ITN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES 7.5, 0.3M NACL, 21% PEG6K, 5MM TCEP
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.889 α = 90 b = 90.304 β = 90 c = 164.347 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 CCD ADSC CCD MIRRORS 2007-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 3.1 50 99.2 0.1 24 9.1 16223 -3
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 3.1 3.34 96.1 0.38 5.5 7.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ITN 3.1 24.42 14268 759 99.2 0.209 0.207 0.2053 0.249 0.2489 RANDOM 49
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 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.202 r_dihedral_angle_4_deg 22.516 r_dihedral_angle_3_deg 20.739 r_dihedral_angle_1_deg 8.24 r_scangle_it 3.582 r_scbond_it 2.021 r_mcangle_it 1.65 r_angle_refined_deg 1.311 r_mcbond_it 0.862 r_symmetry_hbond_refined 0.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.202 r_dihedral_angle_4_deg 22.516 r_dihedral_angle_3_deg 20.739 r_dihedral_angle_1_deg 8.24 r_scangle_it 3.582 r_scbond_it 2.021 r_mcangle_it 1.65 r_angle_refined_deg 1.311 r_mcbond_it 0.862 r_symmetry_hbond_refined 0.424 r_nbtor_refined 0.335 r_nbd_refined 0.295 r_symmetry_vdw_refined 0.212 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.078 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4813 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing