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Crystal structure of EGFR kinase domain T790M mutation in compex with HKI-272
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GS7 PDB ENTRY 2GS7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH7.0, 0.2M LI2SO4, 28% PEG3350, 5MM TCEP, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.087 α = 90 b = 98.989 β = 109.94 c = 73.326 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 CCD ADSC CCD MIRRORS 2006-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 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 3.5 50 91.3 0.18 5.8 2.7 8699 -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 3.5 3.77 93 0.4 2.8 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2GS7 3.5 25 8213 428 90.2 0.253 0.251 0.284 0.2502 RANDOM 45.59
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] 5.96 1.93 -1.03 -3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.842 r_dihedral_angle_3_deg 29.226 r_dihedral_angle_4_deg 25.58 r_scangle_it 2.184 r_mcangle_it 2.06 r_dihedral_angle_1_deg 1.684 r_scbond_it 1.439 r_mcbond_it 1.241 r_angle_refined_deg 1.046 r_nbd_refined 0.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.842 r_dihedral_angle_3_deg 29.226 r_dihedral_angle_4_deg 25.58 r_scangle_it 2.184 r_mcangle_it 2.06 r_dihedral_angle_1_deg 1.684 r_scbond_it 1.439 r_mcbond_it 1.241 r_angle_refined_deg 1.046 r_nbd_refined 0.447 r_chiral_restr 0.399 r_nbtor_refined 0.374 r_xyhbond_nbd_refined 0.356 r_symmetry_vdw_refined 0.319 r_symmetry_hbond_refined 0.147 r_gen_planes_refined 0.022 r_bond_refined_d 0.009 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 4277 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing