4R37

Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acyltransferase from Bacteroides fragilis 9343 with UDP-GlcNAc

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	28 % PEG600, 200 mM Calcium Acetate, 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.403	α = 90
b = 149.403	β = 90
c = 149.403	γ = 90

Symmetry
Space Group	P 41 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 315	Rh coated flat mirror	2014-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.12709	SSRL	BL7-1

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	105.64	99.9	0.052	30	7.1	45186	45186		-3	18.6

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	1.95	99.5		0.357	5.6	7.1	2959

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	PDB entry 1LXA	1.9	38	42852	42852	2289	99.85	0.14928	0.14739	0.18513	RANDOM	21.123

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.379
r_dihedral_angle_4_deg	20.874
r_dihedral_angle_3_deg	12.584
r_dihedral_angle_1_deg	6.724
r_long_range_B_refined	6.366
r_long_range_B_other	6.097
r_scangle_other	4.49
r_scbond_it	3.026
r_scbond_other	3.025
r_mcangle_other	2.285
r_mcangle_it	2.284
r_angle_refined_deg	1.798
r_mcbond_it	1.742
r_mcbond_other	1.726
r_angle_other_deg	1.231
r_chiral_restr	0.105
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3894
Nucleic Acid Atoms
Solvent Atoms	517
Heterogen Atoms	86

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling