8HV1

Crystal structure of EGFR_DMX in complex with covalently bound fragment 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EDQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52920.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Crystal Properties
Matthews coefficientSolvent content
3.3863.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.91α = 90
b = 144.91β = 90
c = 144.91γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98SOLEILPROXIMA 2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2645.8399.70.0610.0640.02123.210.418909
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)RedundancyNumber Unique Reflections (All)
12.262.3296.11.5561.6390.5080.51610

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 REPLACEMENTTHROUGHOUT5EDQ2.4251890999699.880.190670.189140.21884RANDOM61.464
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.489
r_dihedral_angle_3_deg17.853
r_dihedral_angle_4_deg15.64
r_long_range_B_refined14.188
r_long_range_B_other14.187
r_scangle_other9.862
r_mcangle_it9.355
r_mcangle_other9.352
r_scbond_it6.791
r_scbond_other6.788
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.489
r_dihedral_angle_3_deg17.853
r_dihedral_angle_4_deg15.64
r_long_range_B_refined14.188
r_long_range_B_other14.187
r_scangle_other9.862
r_mcangle_it9.355
r_mcangle_other9.352
r_scbond_it6.791
r_scbond_other6.788
r_dihedral_angle_1_deg6.499
r_mcbond_it6.313
r_mcbond_other6.313
r_angle_refined_deg1.578
r_angle_other_deg1.325
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms2406
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing