4RKR

Crystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007, complex with lactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RKQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		Protein: 10 mM bis-tris, 500 mM NaCl, 10% glycerol, 5 mM DTT reservoir: 0.1 M magnesium chloride, 0.1 M MES:HAOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir plus 20 mM lactose; vapor diffusion, sitting drop, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.936	α = 90
b = 124.912	β = 96.51
c = 117.043	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	ADSC QUANTUM 315	MIRRORS	2014-07-10	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	2.2	50	99.1	0.141	0.141	7.5	3		52910		-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	2.2	2.23	98.6		1.4	3

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	4RKQ	2.2	50	51293	1588	98.9	0.17387	0.17142	0.25183	RANDOM	45.889

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]
1.8		-2.3	0.29		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.043
r_scbond_it	20.971
r_scbond_other	20.971
r_scangle_other	20.179
r_long_range_B_refined	18.724
r_long_range_B_other	18.724
r_dihedral_angle_4_deg	17.766
r_dihedral_angle_3_deg	13.34
r_mcbond_other	12.589
r_mcbond_it	12.579
r_mcangle_other	12.343
r_mcangle_it	12.341
r_dihedral_angle_1_deg	5.852
r_angle_refined_deg	1.2
r_angle_other_deg	0.71
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
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	7956
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	92

Software

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