4RYA

Crystal structure of abc transporter solute binding protein AVI_3567 from AGROBACTERIUM VITIS S4, TARGET EFI-510645, with bound D-mannitol

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-MANNITOL), RESERVOIR: 0.085 M TRIS-HCL, PH 8.5, 0.17 M SODIUM ACETATE, 25% PEG3350, 15% (V/V) GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.413	α = 90
b = 61.256	β = 104.01
c = 65.501	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	CCD	RAYONIX MX225HE	MIRRORS	2014-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		APS	31-ID

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	1.5	50	99.3	0.122	12.95	7.5		73250		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	98.4		0.49	4.5	7.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.5	25	69767	2178	98.37	0.13314	0.13204	0.16824	RANDOM	24.318

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]
0.77		-0.99	-0.79		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.747
r_sphericity_free	23.465
r_dihedral_angle_4_deg	19.609
r_sphericity_bonded	14.332
r_dihedral_angle_3_deg	13.48
r_scbond_it	7.253
r_scbond_other	7.252
r_scangle_other	6.365
r_dihedral_angle_1_deg	5.834
r_long_range_B_refined	5.705
r_long_range_B_other	5.705
r_mcangle_other	3.855
r_mcangle_it	3.854
r_mcbond_it	3.367
r_mcbond_other	3.365
r_rigid_bond_restr	3.294
r_angle_refined_deg	1.565
r_angle_other_deg	0.91
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	3234
Nucleic Acid Atoms
Solvent Atoms	466
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing