Experiment: 5BR1

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS S4 (Avi_5305, TARGET EFI-511224) WITH BOUND ALPHA-D-GALACTOSAMINE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Protein (53.5 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-galactosamine); Reservoir (42.1 %(w/v) PEG 4000); Cryoprotection (Reservoir, Pause in air during transfer to liquid N2)

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.781	α = 90
b = 63.701	β = 90
c = 119.575	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2015-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54056

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.85	16.6	87	0.127	0.141	0.059	6.8	4.9		21553			21.92

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	64.8		0.608	0.731	0.397	0.526		2.8	782

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2IOY	1.85	16.499	1.37	20961	1032	84.66	0.1877	0.1827	0.2828	0.2775	34.6342

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.543
f_angle_d	1.397
f_chiral_restr	0.061
f_bond_d	0.013
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2381
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	12

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
HKL-3000	data reduction