7BNT | pdb_00007bnt

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with a predicted ancestral HMA domain of Pik-1 from Oryza spp.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A6W

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.486	α = 90
b = 119.486	β = 90
c = 35.974	γ = 90

Symmetry
Space Group	P 41 21 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		2018-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9700	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	1.32	59.81	96.3	0.068	0.07	0.018	0.999	16.7	14.6		59464

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	1.32	1.34	94.1		2.201	2.285	0.605	0.73		13.9

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	FOURIER SYNTHESIS	THROUGHOUT	5A6W	1.32	59.81	56338	2981	96.1	0.1472	0.1452	0.15	0.1839	0.18	RANDOM	21.866

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]
0.26			0.26		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.633
r_dihedral_angle_4_deg	16.11
r_dihedral_angle_3_deg	11.03
r_dihedral_angle_1_deg	6.659
r_rigid_bond_restr	2.289
r_angle_refined_deg	1.59
r_angle_other_deg	1.467
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.633
r_dihedral_angle_4_deg	16.11
r_dihedral_angle_3_deg	11.03
r_dihedral_angle_1_deg	6.659
r_rigid_bond_restr	2.289
r_angle_refined_deg	1.59
r_angle_other_deg	1.467
r_chiral_restr	0.082
r_bond_refined_d	0.011
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	1737
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
DIALS	data reduction
DIALS	data scaling
REFMAC	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.