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Crystal structure of EGFR kinase domain in complex with AFN941
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M14 PDB ENTRY 1M14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1.2M KNA TARTRATE, 0.1M HEPES 7.5, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.446 α = 90 b = 144.446 β = 90 c = 144.446 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-4 2005-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 2.88 50 100 0.07 33.6 7.1 11527 -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 2.88 3.1 100 0.4 5.4 7.2
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 1M14 2.88 24.08 10912 544 99.7 0.191 0.187 0.185 0.256 0.2525 RANDOM 54.1
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 40.144 r_dihedral_angle_3_deg 20.75 r_dihedral_angle_4_deg 17.328 r_dihedral_angle_1_deg 6.175 r_scangle_it 3.745 r_scbond_it 2.177 r_mcangle_it 1.925 r_angle_refined_deg 1.818 r_mcbond_it 1.006 r_nbtor_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.144 r_dihedral_angle_3_deg 20.75 r_dihedral_angle_4_deg 17.328 r_dihedral_angle_1_deg 6.175 r_scangle_it 3.745 r_scbond_it 2.177 r_mcangle_it 1.925 r_angle_refined_deg 1.818 r_mcbond_it 1.006 r_nbtor_refined 0.331 r_nbd_refined 0.262 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.109 r_bond_refined_d 0.017 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 2395 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing