6CHK | pdb_00006chk

Crystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound TRIS

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.17 M sodium acetate, 0.085 M Tris-HCl, pH 8.5, 25.5% w/v PEG4000, 15% w/v glycerol, cryoprotectant = reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.715	α = 90
b = 108.715	β = 90
c = 125.395	γ = 120

Symmetry
Space Group	H 3 2

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	ADSC QUANTUM 315r	mirrors	2014-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9790	NSLS	X29A

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	1.8	50	100	0.105	0.105	30.2	12.2		26573		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	100		2.5	11.4

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	SAD	THROUGHOUT	1.8	50	25794	775	99.93	0.1453	0.1438	0.16	0.1902	0.2	RANDOM	31.106

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]
-1.16	-0.58		-1.16		3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.617
r_dihedral_angle_4_deg	14.444
r_dihedral_angle_3_deg	12.42
r_dihedral_angle_1_deg	6.185
r_angle_refined_deg	1.633
r_angle_other_deg	0.99
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.617
r_dihedral_angle_4_deg	14.444
r_dihedral_angle_3_deg	12.42
r_dihedral_angle_1_deg	6.185
r_angle_refined_deg	1.633
r_angle_other_deg	0.99
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2062
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELX	phasing
SHELX	model building
ARP/wARP	model building

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.