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Crystal structure of EGFR_TMX in complex with covalently bound fragment 9
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 8.5 292 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Crystal Properties Matthews coefficient Solvent content 3.38 63.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.874 α = 90 b = 144.874 β = 90 c = 144.874 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 110 CMOS BRUKER PHOTON 100 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54184
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 2.69 21.36 99.6 0.139 12.45 8.84 14176
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 2.69 2.79 100 0.4848 3.37 7.97
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 5EDQ 2.69 21.37 13193 678 97.6 0.22174 0.21839 0.2229 0.29019 0.2927 RANDOM 41.047
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 33.457 r_dihedral_angle_3_deg 19.176 r_dihedral_angle_4_deg 14.726 r_long_range_B_other 12.09 r_long_range_B_refined 12.084 r_dihedral_angle_1_deg 6.726 r_scangle_other 6.094 r_mcangle_it 5.987 r_mcangle_other 5.985 r_scbond_it 3.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.457 r_dihedral_angle_3_deg 19.176 r_dihedral_angle_4_deg 14.726 r_long_range_B_other 12.09 r_long_range_B_refined 12.084 r_dihedral_angle_1_deg 6.726 r_scangle_other 6.094 r_mcangle_it 5.987 r_mcangle_other 5.985 r_scbond_it 3.747 r_scbond_other 3.745 r_mcbond_it 3.711 r_mcbond_other 3.711 r_angle_refined_deg 1.533 r_angle_other_deg 1.268 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 2374 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling MOLREP phasing