6FUB | pdb_00006fub

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE 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	7.5	293	0.1M Amino acids (0.2M L-Na-Glutamate; 0.2M Alanine (racemic); 0.2M Glycine; 0.2M Lysine HCl (racemic); 0.2M Serine (racemic)); 0.1M Buffer system 2 (1M sodium HEPES, MOPS (acid)) pH 7.5; 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.023	α = 90
b = 54.345	β = 90.53
c = 48.493	γ = 90

Symmetry
Space Group	P 1 21 1

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		2015-11-28	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)	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	1.3	23.7	99.4	0.071	12.9	7.6		38170

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	1.3	1.32

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	1.3	23.7	36190	1959	99.33	0.14296	0.14087	0.14	0.17854	0.18	RANDOM	21.377

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]
1.66		0.42	-1.03		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.198
r_dihedral_angle_2_deg	31.486
r_sphericity_bonded	17.551
r_dihedral_angle_4_deg	16.307
r_dihedral_angle_3_deg	12.451
r_dihedral_angle_1_deg	6.557
r_long_range_B_refined	5.736
r_long_range_B_other	4.38
r_rigid_bond_restr	3.053
r_mcangle_it	3.008
r_mcangle_other	3.008
r_scangle_other	2.998
r_scbond_it	2.558
r_scbond_other	2.556
r_mcbond_it	2.304
r_mcbond_other	2.301
r_angle_refined_deg	1.925
r_angle_other_deg	1.014
r_chiral_restr	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	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	1352
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms

Software

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