9RSV | pdb_00009rsv

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-Pia with the HMA domain of OsHPP09 from rice (Oryza sativa)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold
experimental model	PDB	6Q76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M MES pH 6.5, 0.2 M ammonium sulphate, 20% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.911	57.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.665	α = 90
b = 93.665	β = 90
c = 72.873	γ = 120

Symmetry
Space Group	P 61 2 2

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		2023-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-1

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	1.65	46.83	99.8	0.037	0.044	0.025	0.999	19.2	5.6		23168

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	1.65	1.68	100		0.874	1.059	0.592	0.837	1.9	5.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	46.83	23139	1151	99.673	0.177	0.176	0.1748	0.2021	0.2007	36.032

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]
0.799	0.399		0.799		-2.591

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.422
r_dihedral_angle_3_deg	14.017
r_lrange_it	10.854
r_lrange_other	10.81
r_scangle_it	8.683
r_scangle_other	8.664
r_dihedral_angle_1_deg	6.788
r_scbond_it	6.001
r_scbond_other	5.993
r_mcangle_it	4.871
r_mcangle_other	4.868
r_dihedral_angle_2_deg	4.706
r_mcbond_it	3.54
r_mcbond_other	3.538
r_angle_refined_deg	2.243
r_angle_other_deg	0.768
r_nbd_other	0.347
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.21
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.167
r_chiral_restr	0.118
r_symmetry_nbtor_other	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_chiral_restr_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1053
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	10

Software

Software
Software Name	Purpose
EDNA	data collection
XDS	data reduction
PHASER	phasing
Aimless	data scaling
REFMAC	refinement