4RK1 | pdb_00004rk1

Crystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose

X-RAY DIFFRACTION

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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: 1 M sodium acetate:HCl, pH 4.6, 1.5 M ammonium chloride, 10 mM D-glucose, cryoprotectant = reservoir + 30% w/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.371	α = 90
b = 95.243	β = 119.47
c = 123.602	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 315r	mirrors	2014-09-05	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	1.9	50	100	0.1	0.1	16.9	5.2		197594		-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	1.9	1.93	95.7		0.93	0.93	1.8	4.8

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	SAD	THROUGHOUT	1.9	50	190152	5684	99.93	0.16012	0.15922	0.1738	0.19234	0.2036	RANDOM	37.347

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]
-1.34		0.03	2.63		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.251
r_long_range_B_other	15.084
r_long_range_B_refined	15.083
r_scangle_other	14.268
r_scbond_it	13.209
r_scbond_other	13.208
r_dihedral_angle_3_deg	12.763
r_dihedral_angle_4_deg	9.884
r_mcangle_it	8.621
r_mcangle_other	8.621
r_mcbond_it	7.803
r_mcbond_other	7.801
r_dihedral_angle_1_deg	5.963
r_angle_refined_deg	1.22
r_angle_other_deg	0.747
r_chiral_restr	0.071
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	12715
Nucleic Acid Atoms
Solvent Atoms	1175
Heterogen Atoms	81

Software

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