1M6B

Structure of the HER3 (ERBB3) Extracellular Domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293pH 9.0, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal Properties
Matthews coefficientSolvent content
3.3363.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 236.26α = 90
b = 49.62β = 125.56
c = 190.86γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4ANSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.6205436048669

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.6205436048669261494.550.23810.235150.29391RANDOM17.631
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]
-0.060.14-0.160.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.369
r_scangle_it4.114
r_scbond_it2.256
p_angle_d1.593
r_angle_refined_deg1.593
r_mcangle_it1.143
r_mcbond_it0.566
r_nbd_refined0.232
r_symmetry_vdw_refined0.227
r_xyhbond_nbd_refined0.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.369
r_scangle_it4.114
r_scbond_it2.256
p_angle_d1.593
r_angle_refined_deg1.593
r_mcangle_it1.143
r_mcbond_it0.566
r_nbd_refined0.232
r_symmetry_vdw_refined0.227
r_xyhbond_nbd_refined0.182
r_symmetry_hbond_refined0.147
r_chiral_restr0.103
p_bond_d0.013
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8684
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms243

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement