6AAL

Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Arginine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	2M Ammonium sulphate, 0.1M Sodium acetate trihydrate pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.342	α = 90
b = 86	β = 90
c = 123.832	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	MARRESEARCH		2017-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.6	70.64	98.6	0.15	9.5	4.2		15666			41.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	96.9		0.8	1.23	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2YLN	2.6	70.64	14811	826	98.71	0.20509	0.20018	0.29013	RANDOM	40.787

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]
0.31			0.13		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.662
r_dihedral_angle_4_deg	18.314
r_dihedral_angle_3_deg	18.075
r_dihedral_angle_1_deg	7.467
r_long_range_B_other	6.567
r_long_range_B_refined	6.566
r_scangle_other	4.48
r_mcangle_it	4.179
r_mcangle_other	4.178
r_scbond_it	2.896
r_scbond_other	2.896
r_mcbond_it	2.696
r_mcbond_other	2.695
r_angle_refined_deg	1.618
r_angle_other_deg	0.843
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3760
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MoRDa	phasing