4KWU

1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 from Listeria monocytogenes EGD-e in complex with alpha-D-glucose, beta-D-glucose, magnesium and calcium

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	crystallization conditions - 0.2 M magnesium formate, 20% (w/v) PEG3350 (The JCSG+ suite: A5), protein - 7.3 mg/mL in 10 mM Tris-HCl pH8.3 500 mM NaCl 5 mM BME, soak/cryo - crystallization conditions + 50% glucose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.125	α = 90
b = 102.962	β = 104.93
c = 75.006	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 300 mm CCD	Mirror	2013-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0782	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	30	98.5	0.076	15.8	3.6	94351	94351		-3	22.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	97.5		0.568	2.6	3.6	4671

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4KMQ	1.9	29.92	89621	89621	4730	98.36	0.13686	0.13508	0.17075	RANDOM	20.468

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]
0.43		1.82	0.2		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.062
r_dihedral_angle_4_deg	15.047
r_dihedral_angle_3_deg	10.189
r_dihedral_angle_1_deg	4.417
r_scangle_it	3.589
r_scbond_it	2.335
r_angle_refined_deg	1.573
r_mcangle_it	1.294
r_angle_other_deg	0.872
r_mcbond_it	0.729

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.062
r_dihedral_angle_4_deg	15.047
r_dihedral_angle_3_deg	10.189
r_dihedral_angle_1_deg	4.417
r_scangle_it	3.589
r_scbond_it	2.335
r_angle_refined_deg	1.573
r_mcangle_it	1.294
r_angle_other_deg	0.872
r_mcbond_it	0.729
r_mcbond_other	0.231
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8335
Nucleic Acid Atoms
Solvent Atoms	1232
Heterogen Atoms	129

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.