4XFK | pdb_00004xfk

Crystal structure of Leucine-, Isoleucine-, Valine-, Threonine-, and Alanine-binding protein from Brucella ovis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		structure initially solved via Iodide SAD in oP crystal form, this model was used for Molecular Replacement into mP crystal form

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	290	Microlytics MCSG1 screen, a2: 100mM CHES/NaOH, pH 9.5, 30% PEG 3000; BrovA.17370.a.B2.PS02137 at 25mg/ml; cryo: Al's oil; tray 257610a2, puck wln2-3; crystal #2 was used for phasing
2	VAPOR DIFFUSION, SITTING DROP	7.5	290	Microlytics MCSG1 screen, c10: 1M LiCl, 100mM Na-acetate, 30% PEG 6000; the crystal was incubated in two cryo/phasing solution for 30sec each: 4.5ul reservoir + 0.5ul of 2.5M NaI in ethylene glycol, and 4ul reservoir + 1ul of 2.5M NaI in ethylene glycol, final 500mM NaI and 20% ethylene glycol; this is a different crystal form: P212121 with a=60.7AA, b=67.26AA, c=94.5AA; this crystal was used for phasing; tray 257610c10, puck ilg3-2

Crystal Properties
Matthews coefficient	Solvent content
2.05	40
2.24	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.12	α = 90
b = 46.39	β = 101.62
c = 62.4	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	RAYONIX MX-225		2010-11-12	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	RIGAKU SATURN 944+		2010-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.3	50	97.9	0.046	0.054	17.96	3.8	85749	83917		-3	10.36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.33	96.1		0.517	0.605	2.49	3.7

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	structure initially solved via Iodide SAD in oP crystal form, this model was used for Molecular Replacement into mP crystal form	1.3	30.424	1.35	83914	2009	97.9	0.1379	0.1373	0.14	0.1611	0.16	Random selection	14.3044

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	11.79
f_angle_d	1.098
f_chiral_restr	0.075
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2921
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
WARP	model building
Coot	model building
PDB_EXTRACT	data extraction

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.