5IXQ

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429819% PEG 3350, 0.2 M MgCl2, 0.1 M citric acid pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.6854.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.282α = 90
b = 148.282β = 90
c = 57.93γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000010SLSX10SA

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
11.86128.4299.80.055116.720.361813-380
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.9798.6219.1

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 SYNTHESISTHROUGHOUT5IXO1.86128.4258551298899.990.184150.182930.20729RANDOM79.083
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]
0.430.220.43-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.795
r_dihedral_angle_4_deg17.233
r_dihedral_angle_3_deg12.744
r_dihedral_angle_1_deg6.349
r_long_range_B_refined6.205
r_long_range_B_other6.205
r_scangle_other5.534
r_scbond_it3.852
r_scbond_other3.851
r_mcangle_it3.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.795
r_dihedral_angle_4_deg17.233
r_dihedral_angle_3_deg12.744
r_dihedral_angle_1_deg6.349
r_long_range_B_refined6.205
r_long_range_B_other6.205
r_scangle_other5.534
r_scbond_it3.852
r_scbond_other3.851
r_mcangle_it3.008
r_mcangle_other3.008
r_mcbond_it2.563
r_mcbond_other2.563
r_angle_refined_deg1.691
r_angle_other_deg1.12
r_chiral_restr0.096
r_bond_refined_d0.012
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 Atoms4611
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACrefinement