6FUD | pdb_00006fud

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikA 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	0.12M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol); 0.1M Buffer system 2 (1M sodium HEPES, MOPS (acid)) pH 7.5; 50% v/v Precipitant mix 4 (25%v/v MPD; 25%v/v PEG 1000; 25%v/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.07	α = 90
b = 54.44	β = 104.43
c = 46.64	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	34.76	99.3	0.043	21.5	7.8		33854

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	1.33

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	34.76	33854	1720	99.25	0.12719	0.12542	0.13	0.16191	0.16	RANDOM	22.458

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]
-1.68		0.67	-0.06		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.372
r_dihedral_angle_2_deg	32.269
r_dihedral_angle_4_deg	14.647
r_sphericity_bonded	14.304
r_dihedral_angle_3_deg	12.12
r_dihedral_angle_1_deg	6.968
r_long_range_B_refined	5.667
r_long_range_B_other	5.665
r_scangle_other	4.994
r_scbond_it	3.996
r_scbond_other	3.991
r_mcangle_it	3.522
r_mcangle_other	3.52
r_rigid_bond_restr	2.83
r_mcbond_it	2.759
r_mcbond_other	2.742
r_angle_refined_deg	1.775
r_angle_other_deg	0.984
r_chiral_restr	0.115
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
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	1239
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms

Software

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