1Z15

Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein in superopen form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7.3	293	12.5% PEG 6000, potassium chloride, sodium choloride, sodium azide, potassium acetate, sodium citrate, pH 7.3, MICRODIALYSIS, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.21	α = 90
b = 65.29	β = 90
c = 109.61	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	293	AREA DETECTOR	SDMS		1990-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	50	96	0.069	0.069	9.8	4	44773	44773	1	1	17.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.75	89		0.277	0.277	1.9	4	4655

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2LIV	1.7	6	42957	42957	4319	95.8	0.185	0.237	RANDOM	26.1

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]
1.48			2.35		-3.83

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.5
c_scangle_it	4.31
c_scbond_it	2.91
c_mcangle_it	2.3
c_mcbond_it	1.61
c_angle_deg	1.5
c_improper_angle_d	1.46
c_bond_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2591
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
SDMS	data reduction
SDMS	data scaling
MERLOT	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.