3QWQ

Crystal structure of the extracellular domain of the epidermal growth factor receptor in complex with an adnectin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NQLEGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509
experimental modelPDB 1FNFEGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1729360% Tacsimate, pH 7.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.8267.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68α = 90
b = 72.1β = 90
c = 262γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002009-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-GAPS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.755099.60.06923.14.83428571.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.851000.5523.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTEGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-15092.7549.4734224105899.380.2040.2020.246RANDOM64.63
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]
-3.2678-3.41566.6834
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion20.5
t_omega_torsion3.35
t_angle_deg1.4
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion20.5
t_omega_torsion3.35
t_angle_deg1.4
t_bond_d0.01
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 AtomsNumber
Protein Atoms5359
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms237

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTERrefinement