5IXT

The crystal structure of the Arabidopsis receptor kinase HAESA LRR ectdomain in complex with a N-terminal extended IDA peptide hormone ligand.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429823% PEG 3350,0.2M MgCl2,0.1M citric acid pH4
Crystal Properties
Matthews coefficientSolvent content
2.6954.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.921α = 90
b = 148.921β = 90
c = 58.022γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.999980SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.94128.9799.40.035120.911.254201-381.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.942.0697.92.411.1

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5IXO1.94128.9751557264499.410.180680.179260.20763RANDOM80.66
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]
1.180.591.18-3.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.984
r_dihedral_angle_4_deg18.05
r_dihedral_angle_3_deg13.654
r_long_range_B_refined6.698
r_long_range_B_other6.698
r_dihedral_angle_1_deg6.472
r_scangle_other5.878
r_scbond_it4.076
r_scbond_other4.075
r_mcangle_it3.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.984
r_dihedral_angle_4_deg18.05
r_dihedral_angle_3_deg13.654
r_long_range_B_refined6.698
r_long_range_B_other6.698
r_dihedral_angle_1_deg6.472
r_scangle_other5.878
r_scbond_it4.076
r_scbond_other4.075
r_mcangle_it3.195
r_mcangle_other3.194
r_mcbond_other2.695
r_mcbond_it2.694
r_angle_refined_deg1.8
r_angle_other_deg1.124
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4607
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing