6Q76 | pdb_00006q76

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-Pia with the HMA domain of Pikp-1 from rice (Oryza sativa)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2MYW	2MYW, 5A6P
experimental model	PDB	5A6P	2MYW, 5A6P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1-Butanol; 0.2 M 1,2-Propanediol; 0.2 M 2-Propanol; 0.2 M 1,4-Butanediol; 0.2 M 1,3-Propanediol), 0.1 M Buffer System 1 (1.0 M imidazole; MES monohydrate (acid), pH 6.5) and 50 % v/v Precipitant Mix 2 (40 % v/v Ethylene glycol; 20 % w/v PEG 8000)

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.844	α = 90
b = 53.444	β = 90
c = 117.81	γ = 90

Symmetry
Space Group	P 2 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 PILATUS 6M		2017-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.9	48.72	100	0.057	0.99	19.7	12.6		18107

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	100		0.81		13.3

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	2MYW, 5A6P	1.9	48.72	17101	962	99.93	0.2053	0.2031	0.21	0.2451	0.25	RANDOM	52.819

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]
4.52			-2.04		-2.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.113
r_dihedral_angle_3_deg	16.285
r_dihedral_angle_4_deg	14.84
r_dihedral_angle_1_deg	6.6
r_angle_refined_deg	1.501
r_angle_other_deg	0.94
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.113
r_dihedral_angle_3_deg	16.285
r_dihedral_angle_4_deg	14.84
r_dihedral_angle_1_deg	6.6
r_angle_refined_deg	1.501
r_angle_other_deg	0.94
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1066
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.