5IYV

Crystal structure of the Arabidopsis receptor kinase HAESA LRR ectdomain in complex with the peptide hormone IDL1.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429822% PEG 3350, 0.2 M MgCl2, 0.1 M citric acid pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.8556.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.181α = 90
b = 150.181β = 90
c = 60.07γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-07-14MSINGLE 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
12.565099.50.054125.971525124-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.562.7298.81.9114.6

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 SYNTHESISTHROUGHOUT5IXO2.5649.1623835128899.470.192940.190910.23107RANDOM89.4
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]
-4-2-412.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.189
r_dihedral_angle_4_deg15.62
r_dihedral_angle_3_deg13.603
r_long_range_B_refined8.164
r_long_range_B_other8.164
r_dihedral_angle_1_deg6.306
r_scangle_other5.209
r_mcangle_it3.368
r_mcangle_other3.367
r_scbond_it3.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.189
r_dihedral_angle_4_deg15.62
r_dihedral_angle_3_deg13.603
r_long_range_B_refined8.164
r_long_range_B_other8.164
r_dihedral_angle_1_deg6.306
r_scangle_other5.209
r_mcangle_it3.368
r_mcangle_other3.367
r_scbond_it3.317
r_scbond_other3.315
r_mcbond_it2.216
r_mcbond_other2.216
r_angle_refined_deg1.479
r_angle_other_deg1.047
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms4555
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms180

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement