6FMB | pdb_00006fmb

Crystal structure of the BEC1054 RNase-like effector from the fungal pathogen Blumeria graminis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	Purified CSEP0064/BEC1054 was dialysed into crystallisation buffer (10 mM Tris, 150 mM NaCl, pH 7.0) and concentrated to 10 mg/ml for crystallisation. Commercially available solution conditions for crystallisation (Hampton Research,CA, USA) were screened. The protein was combined with the mother liquor on a 1:1 ratio in 200 nl drops. Crystals obtained in 0.1 M sodium acetate buffer pH 5.0, supplemented with 30% PEG 4000, 0.4 M (NH4)2SO4 were cryoprotected with 30% glycerol and flash frozen for data collection.

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.52	α = 90
b = 60.52	β = 90
c = 78.28	γ = 120

Symmetry
Space Group	P 62 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M-F		2015-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92, 0.95	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.3	52.51	99.5	0.998	23.4	6		21286

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.34			0.996	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.3	52.41	20158	1092	99.49	0.14536	0.14374	0.15	0.17645	0.18	RANDOM	15.399

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]
0.02	0.01		0.02		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	23.595
r_dihedral_angle_2_deg	22.996
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_3_deg	12.299
r_sphericity_bonded	8.019
r_rigid_bond_restr	6.813
r_dihedral_angle_1_deg	6.649
r_long_range_B_refined	3.517
r_long_range_B_other	3.185
r_scangle_other	2.637
r_mcangle_other	2.29
r_mcangle_it	2.283
r_scbond_it	2.178
r_scbond_other	2.176
r_mcbond_it	1.77
r_mcbond_other	1.77
r_angle_refined_deg	1.568
r_angle_other_deg	1.114
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
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	744
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
SHARP	phasing