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Crystal structure of EGFR_wt in complex with covalently bound fragment 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 0.1M TRIS pH 7.0, 1.2M Sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.41 63.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.453 α = 90 b = 145.453 β = 90 c = 145.453 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 PIXEL DECTRIS PILATUS 6M-F 2019-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.798 59.381 90.6 0.124 0.13 0.039 0.999 15.4 10.8 11590
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.798 2.88 56.2 2.124 2.219 0.641 0.48 1.3 11.9
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 5EDQ 2.8 25 11019 545 90.58 0.1794 0.17741 0.21645 0.2021 RANDOM 80.348
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 39.065 r_dihedral_angle_3_deg 18.542 r_long_range_B_refined 15.083 r_long_range_B_other 15.082 r_dihedral_angle_4_deg 11.512 r_scangle_other 10.196 r_mcangle_it 9.775 r_mcangle_other 9.775 r_dihedral_angle_1_deg 7.489 r_scbond_it 6.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.065 r_dihedral_angle_3_deg 18.542 r_long_range_B_refined 15.083 r_long_range_B_other 15.082 r_dihedral_angle_4_deg 11.512 r_scangle_other 10.196 r_mcangle_it 9.775 r_mcangle_other 9.775 r_dihedral_angle_1_deg 7.489 r_scbond_it 6.578 r_scbond_other 6.576 r_mcbond_it 6.503 r_mcbond_other 6.47 r_angle_refined_deg 1.478 r_angle_other_deg 1.243 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2346 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing