4RK5 | pdb_00004rk5

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.16 M calcium acetate, 0.08 M sodium cacodylate, pH 6.5, 14.4% PEG8000, 20% glycerol, cryoprotectant = reservoir + 100 mM sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.754	α = 90
b = 108.754	β = 90
c = 125.763	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		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	1.35	50	100	0.051	0.051	39	9.1		62512		-3

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	1.35	1.37	100		0.88	0.88	2.1	7.8

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	MR	THROUGHOUT	1.35	44.1	60647	1865	99.94	0.11003	0.10905	0.1379	0.14093	0.1585	RANDOM	28.146

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]
-0.02	-0.01		-0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	34.803
r_dihedral_angle_2_deg	34.693
r_sphericity_bonded	20.354
r_dihedral_angle_4_deg	13.154
r_dihedral_angle_3_deg	12.436
r_scbond_it	10.583
r_scbond_other	10.58
r_scangle_other	9.969
r_long_range_B_refined	8.714
r_long_range_B_other	8.713
r_mcangle_it	6.307
r_mcangle_other	6.305
r_mcbond_it	6.19
r_mcbond_other	6.189
r_rigid_bond_restr	6
r_dihedral_angle_1_deg	5.893
r_angle_refined_deg	1.929
r_angle_other_deg	1.648
r_chiral_restr	0.121
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2087
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	28

Software

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