5IYX

Crystal structure of the Arabidopsis receptor kinase HAESA in complex with the peptide hormone IDA and the co-receptor SERK1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IXO5IXO, 4LSC
experimental modelPDB 4LSC5IXO, 4LSC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429818% PEG 8,000, 0.2 M MgCl2, 0.1 M citric acid pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.8156.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.507α = 90
b = 100.456β = 90
c = 142.759γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000020SLSX10SA

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
12.435099.40.1070.99916.19.841023-359.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.432.5796.41.969.3

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 REPLACEMENTTHROUGHOUT5IXO, 4LSC2.4347.3838969205199.380.194780.192660.23435RANDOM59.535
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]
-2.74-2.14.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.695
r_dihedral_angle_4_deg16.808
r_dihedral_angle_3_deg13.116
r_dihedral_angle_1_deg6.066
r_long_range_B_other6.025
r_long_range_B_refined6.024
r_scangle_other2.564
r_scbond_it1.557
r_scbond_other1.556
r_mcangle_it1.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.695
r_dihedral_angle_4_deg16.808
r_dihedral_angle_3_deg13.116
r_dihedral_angle_1_deg6.066
r_long_range_B_other6.025
r_long_range_B_refined6.024
r_scangle_other2.564
r_scbond_it1.557
r_scbond_other1.556
r_mcangle_it1.514
r_mcangle_other1.514
r_angle_refined_deg1.41
r_angle_other_deg1.038
r_mcbond_it0.918
r_mcbond_other0.917
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms6066
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms176

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing