6R8K | pdb_00006r8k

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with an engineered 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	6G10

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.12M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2- Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1M Buffer system 1 (1M Imidazole, MES monohydrate (acid)) pH 6.5, 50% v/v Precipitant mix 4 (25%v/v MPD, 25%v/v PEG 1000, 25%v/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.79	α = 90
b = 65.33	β = 90
c = 75.86	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		2017-04-29	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)	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	1.6	32.8	100	0.081	0.084	0.024	0.99	16.1	12.8		20294

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	1.6	1.63	100		0.971	1.01	0.38	0.866	2.6	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	6G10	1.6	32.8	19242	1001	99.92	0.1983	0.1966	0.21	0.232	0.24	RANDOM	25.609

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]
-0.87			0.01		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.977
r_dihedral_angle_4_deg	18.226
r_dihedral_angle_3_deg	17.467
r_dihedral_angle_1_deg	6.801
r_angle_refined_deg	1.495
r_angle_other_deg	1.339
r_chiral_restr	0.063
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.977
r_dihedral_angle_4_deg	18.226
r_dihedral_angle_3_deg	17.467
r_dihedral_angle_1_deg	6.801
r_angle_refined_deg	1.495
r_angle_other_deg	1.339
r_chiral_restr	0.063
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1248
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
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.