7A8W | pdb_00007a8w

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

X-RAY DIFFRACTION

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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	0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 2 (Sodium HEPES; MOPS (acid)) pH 7.5; 37.5% v/v Precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.784	α = 90
b = 80.205	β = 90
c = 105.683	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		2017-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.15	46.17	99.9	0.053	0.055	0.015	1	23.9	13.2		31604

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	2.15	2.22	99.8		0.996	1.034	0.278	0.925	2.3	13.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5A6W	2.15	44.165	31548	1510	99.921	0.227	0.2241	0.23	0.2722	0.27	63.54

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]
-4.396			7.349		-2.953

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.047
r_dihedral_angle_4_deg	19.723
r_dihedral_angle_3_deg	16.847
r_lrange_other	9.148
r_lrange_it	9.146
r_dihedral_angle_1_deg	7.436
r_scangle_it	7.304
r_scangle_other	7.294
r_mcangle_it	6.291
r_mcangle_other	6.291
r_scbond_it	5.117
r_scbond_other	5.114
r_mcbond_it	4.631
r_mcbond_other	4.623
r_angle_refined_deg	1.479
r_angle_other_deg	1.183
r_nbd_other	0.21
r_nbd_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.179
r_symmetry_nbd_refined	0.172
r_xyhbond_nbd_refined	0.159
r_nbtor_refined	0.152
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.056
r_symmetry_xyhbond_nbd_other	0.052
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	3443
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data processing
Aimless	data scaling
PHASER	phasing
REFMAC	refinement