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Crystal structure of EGFR kinase domain in complex with an irreversible inhibitor 34-jab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ITW PDB ENTRY 2ITW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1.2M NAK TARTRATE, 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 3.4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.876 α = 90 b = 145.876 β = 90 c = 145.876 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 CCD MIRRORS 2006-04-22 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 2.95 50 95.1 0.08 25.3 7.2 10540 -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 2.95 3.18 75.2 0.4 5.4 7.3
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 2ITW 3 25 9776 732 100 0.194 0.19 0.1901 0.246 0.2438 RANDOM 48.35
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 40.952 r_dihedral_angle_3_deg 20.549 r_dihedral_angle_4_deg 20.117 r_dihedral_angle_1_deg 5.583 r_scangle_it 3.484 r_scbond_it 2.01 r_mcangle_it 1.741 r_angle_refined_deg 1.58 r_mcbond_it 0.915 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.952 r_dihedral_angle_3_deg 20.549 r_dihedral_angle_4_deg 20.117 r_dihedral_angle_1_deg 5.583 r_scangle_it 3.484 r_scbond_it 2.01 r_mcangle_it 1.741 r_angle_refined_deg 1.58 r_mcbond_it 0.915 r_nbtor_refined 0.329 r_nbd_refined 0.267 r_symmetry_hbond_refined 0.239 r_symmetry_vdw_refined 0.232 r_xyhbond_nbd_refined 0.215 r_chiral_restr 0.193 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 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 2447 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing