6FU9 | pdb_00006fu9

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikm-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	8.5	293	0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene-glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol); 0.1M Buffer system 3 (1M Tris (base); BICINE) pH 8.5; 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.09	α = 90
b = 87.13	β = 90
c = 103.84	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		2016-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.91680	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.2	29.04	98.5	0.049	21.7	11.9		104301

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.23

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	5A6W	1.2	29.04	99199	5033	98.33	0.15025	0.14852	0.16	0.18435	0.19	RANDOM	22.92

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]
-1.35			-0.78		2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.921
r_sphericity_free	30.754
r_dihedral_angle_4_deg	18.807
r_sphericity_bonded	16.539
r_dihedral_angle_3_deg	12.501
r_dihedral_angle_1_deg	6.473
r_long_range_B_refined	5.685
r_long_range_B_other	5.614
r_mcangle_it	4.323
r_mcangle_other	4.322
r_scangle_other	4.253
r_rigid_bond_restr	3.752
r_scbond_other	3.62
r_scbond_it	3.619
r_mcbond_other	3.327
r_mcbond_it	3.326
r_angle_refined_deg	1.902
r_angle_other_deg	1.112
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2573
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms

Software

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