6MLJ

Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S70A mutant from Salmonella typhimurium complexed with arginine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LAF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291.15	0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.087	α = 90
b = 37.241	β = 90.01
c = 102.036	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	PIXEL	DECTRIS PILATUS 200K	Osmic VariMax Cu-HF	2018-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.6	38.34	99.1	0.101	0.991	18.3	4.6		58580			13.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	99		0.259	0.939	6.8	2.8

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	1LAF	1.6	38.34	57275	1002	99.13	0.1923	0.19174	0.2236	RANDOM	16.643

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]
4.5		5.79	-6.58		2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.833
r_dihedral_angle_4_deg	16.717
r_dihedral_angle_3_deg	15.182
r_dihedral_angle_1_deg	7.285
r_long_range_B_refined	4.611
r_long_range_B_other	4.531
r_scangle_other	3.007
r_mcangle_it	2.546
r_mcangle_other	2.546
r_scbond_it	2.012
r_scbond_other	2.012
r_angle_refined_deg	1.909
r_mcbond_it	1.734
r_mcbond_other	1.733
r_angle_other_deg	1.417
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
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	3621
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing