5IYX | pdb_00005iyx

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IXO	5IXO, 4LSC
experimental model	PDB	4LSC	5IXO, 4LSC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	18% PEG 8,000, 0.2 M MgCl2, 0.1 M citric acid pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.25

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2014-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000020	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.43	50	99.4	0.107	0.999	16.1	9.8		41023		-3	59.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.43	2.57	96.4		1.96	9.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5IXO, 4LSC	2.43	47.38	38969	2051	99.38	0.19478	0.19266	0.2	0.23435	0.23	RANDOM	59.535

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			-2.1		4.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.695
r_dihedral_angle_4_deg	16.808
r_dihedral_angle_3_deg	13.116
r_dihedral_angle_1_deg	6.066
r_long_range_B_other	6.025
r_long_range_B_refined	6.024
r_scangle_other	2.564
r_scbond_it	1.557
r_scbond_other	1.556
r_mcangle_it	1.514
r_mcangle_other	1.514
r_angle_refined_deg	1.41
r_angle_other_deg	1.038
r_mcbond_it	0.918
r_mcbond_other	0.917
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	6066
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	176

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing