4RY0

Crystal structure of ribose transporter solute binding protein RHE_PF00037 from Rhizobium etli CFN 42, TARGET EFI-511357, in complex with D-ribose

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-RIBOSE); RESERVOIR: 0.2 M CALCIUM CHLORIDE, 0.1 M TRIS-HCL, PH 8.5, 20% (w/v) PEG 4000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% D-GLUCOSE SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.11	α = 90
b = 36.766	β = 117.91
c = 95.48	γ = 90

Symmetry
Space Group	C 1 2 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	1.4	50	98	0.103	22.2	7.5		57304		-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	1.4	1.42	96.6		0.8	2.57	7.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.4	24	53653	1724	97.66	0.1446	0.14341	0.18106	RANDOM	19.268

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]
-0.65		-1.08	3.84		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.674
r_sphericity_free	30.549
r_sphericity_bonded	15.754
r_dihedral_angle_3_deg	14.736
r_dihedral_angle_4_deg	10.484
r_scbond_it	7.959
r_scbond_other	7.959
r_scangle_other	6.98
r_long_range_B_refined	6.434
r_long_range_B_other	6.34
r_dihedral_angle_1_deg	5.661
r_rigid_bond_restr	4.404
r_mcangle_other	3.337
r_mcangle_it	3.314
r_mcbond_other	3.232
r_mcbond_it	3.196
r_angle_refined_deg	1.537
r_angle_other_deg	1.448
r_chiral_restr	0.09
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	2120
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	12

Software

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