7QPX | pdb_00007qpx

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with an engineered HMA domain of Pikp-1 (Pikp-SNK-EKE) from rice (Oryza sativa)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7A8W

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.353	α = 90
b = 83.13	β = 90
c = 107.035	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 PILATUS 6M		2018-02-09	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	2.05	46.71	99.8	0.081	0.085	0.027	0.999	15.2	9.9		37795

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	2.05	2.11	99.4		1.048	1.103	0.34	0.838		10.1

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	7A8W	2.05	46.71	35848	1898	99.61	0.2056	0.2044	0.21	0.2266	0.23	RANDOM	43.89

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]
-2.41			1.68		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.527
r_dihedral_angle_3_deg	16.108
r_dihedral_angle_4_deg	15.216
r_dihedral_angle_1_deg	7.261
r_angle_refined_deg	1.519
r_angle_other_deg	1.23
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.527
r_dihedral_angle_3_deg	16.108
r_dihedral_angle_4_deg	15.216
r_dihedral_angle_1_deg	7.261
r_angle_refined_deg	1.519
r_angle_other_deg	1.23
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3458
Nucleic Acid Atoms
Solvent Atoms	203
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.