8PFD

Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the von Willebrand Factor Type A domain of the proteasomal ubiquitin receptor Rpn10 from Arabidopsis thaliana

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.391	α = 90
b = 68.599	β = 92.78
c = 49.851	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER2 XE 16M		2021-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9796	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.17	68.6	100	0.118	0.122	0.033	0.999	10.9	13.8		15199

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.24		99.9	2.599	2.7	0.729	0.436		13.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.17	49.84	14486	697	99.99	0.20035	0.19791	0.25225	RANDOM	59.824

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]
-0.32		0.42	-1.29		1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.891
r_dihedral_angle_3_deg	15.302
r_dihedral_angle_4_deg	13.347
r_dihedral_angle_1_deg	7.558
r_long_range_B_refined	4.398
r_long_range_B_other	4.396
r_scangle_other	2.427
r_mcangle_it	2.285
r_mcangle_other	2.285
r_scbond_it	1.512
r_scbond_other	1.512
r_mcbond_it	1.509
r_mcbond_other	1.509
r_angle_refined_deg	1.442
r_angle_other_deg	1.184
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	2200
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing