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Crystal Structure of EGFR T790M mutant in complex with naquotinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Hepes-Na 7.0-7.5, 1.3-1.5M potassium sodium tartrate
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.64 α = 90 b = 144.64 β = 90 c = 144.64 γ = 90
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 270 2011-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 3.25 102.28 99.9 0.107 43.61 10.2 8074 -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 3.25 3.32 100 0.414 9.75 10.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3IKA 3.25 102.28 7695 372 99.73 0.19728 0.1952 0.1979 0.24021 0.2363 RANDOM 65.715
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 r_dihedral_angle_2_deg 42.061 r_dihedral_angle_3_deg 23.592 r_dihedral_angle_4_deg 22.484 r_long_range_B_refined 15.502 r_long_range_B_other 15.501 r_mcangle_it 8.819 r_mcangle_other 8.816 r_scangle_other 8.619 r_scbond_it 5.587 r_mcbond_it 5.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.061 r_dihedral_angle_3_deg 23.592 r_dihedral_angle_4_deg 22.484 r_long_range_B_refined 15.502 r_long_range_B_other 15.501 r_mcangle_it 8.819 r_mcangle_other 8.816 r_scangle_other 8.619 r_scbond_it 5.587 r_mcbond_it 5.548 r_mcbond_other 5.53 r_scbond_other 5.527 r_dihedral_angle_1_deg 5.157 r_angle_refined_deg 1.711 r_angle_other_deg 1.132 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.003 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 2380 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing