3N0W | pdb_00003n0w

Crystal structure of a branched chain amino acid ABC transporter periplasmic ligand-binding protein (Bxe_C0949) from BURKHOLDERIA XENOVORANS LB400 at 1.88 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.86	293	14.0000% polyethylene glycol monomethyl ether 2000, 0.0100M nickel (II) chloride, 0.1M TRIS pH 8.86, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.545	α = 90
b = 58.269	β = 98.96
c = 145.338	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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2010-01-24	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97915,0.97898	SSRL	BL9-2

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	1.88	29.134	91.9	0.07	6.93			62570		-3	23.278

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)
	1.9	1.97	57.3		0.558	1.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.88	29.134	62555	3167	95.66	0.193	0.191	0.19	0.233	0.23	RANDOM	28.782

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]
1.44		0.19	-0.79		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.095
r_dihedral_angle_4_deg	22.256
r_dihedral_angle_3_deg	14.75
r_dihedral_angle_1_deg	5.861
r_scangle_it	3.34
r_scbond_it	2.194
r_angle_refined_deg	1.517
r_angle_other_deg	1.443
r_mcangle_it	1.291
r_mcbond_it	0.749

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.095
r_dihedral_angle_4_deg	22.256
r_dihedral_angle_3_deg	14.75
r_dihedral_angle_1_deg	5.861
r_scangle_it	3.34
r_scbond_it	2.194
r_angle_refined_deg	1.517
r_angle_other_deg	1.443
r_mcangle_it	1.291
r_mcbond_it	0.749
r_mcbond_other	0.164
r_chiral_restr	0.094
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5637
Nucleic Acid Atoms
Solvent Atoms	729
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.