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Crystal structure of the extracellular domain of the epidermal growth factor receptor in complex with an adnectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NQL EGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509 experimental model PDB 1FNF EGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 60% Tacsimate, pH 7.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.82 67.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68 α = 90 b = 72.1 β = 90 c = 262 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-300 2009-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
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 2.75 50 99.6 0.069 23.1 4.8 34285 71.5
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 2.75 2.85 100 0.552 3.1 5
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 EGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509 2.75 49.47 34224 1058 99.38 0.204 0.202 0.2096 0.246 0.2503 RANDOM 64.63
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] -3.2678 -3.4156 6.6834
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.5 t_omega_torsion 3.35 t_angle_deg 1.4 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.5 t_omega_torsion 3.35 t_angle_deg 1.4 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5359 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 237
Software Software Software Name Purpose BUSTER-TNT refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing BUSTER refinement