4RXT | pdb_00004rxt

Crystal structure of carbohydrate transporter solute binding protein Arad_9553 from Agrobacterium Radiobacter, Target EFI-511541, in complex with D-arabinose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-ARABINOSE); RESERVOIR: 0.1 M TRIS-HCL, PH 8.5, 2.5 M AMMONIUM SULFATE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.873	α = 90
b = 36.244	β = 110.01
c = 62.1	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	1.35	50	99.1	0.108	11.3	4.4		55996		-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	1.35	1.37	99.2		0.89	2.4	4.2

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	1.35	50	53008	1633	98.63	0.15747	0.15597	0.17	0.20547	0.21	RANDOM	20.363

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]
-1.32		-1.07	4.53		-1.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.452
r_sphericity_free	38.31
r_dihedral_angle_4_deg	22.131
r_sphericity_bonded	16.011
r_dihedral_angle_3_deg	13.694
r_scbond_other	7.127
r_scbond_it	7.125
r_scangle_other	6.634
r_long_range_B_refined	6.564
r_long_range_B_other	6.563
r_dihedral_angle_1_deg	5.615
r_rigid_bond_restr	4.527
r_mcangle_other	3.1
r_mcangle_it	3.092
r_mcbond_it	2.786
r_mcbond_other	2.781
r_angle_refined_deg	1.597
r_angle_other_deg	1.198
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
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	2149
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	10

Software

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