6I46 | pdb_00006i46

Structure of P. aeruginosa LpxC with compound 8: (2RS)-4-(5-(2-Fluoro-4-methoxyphenyl)-2-oxooxazol-3(2H)-yl)-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	26-30% (w/v) PEG 4000, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.754	α = 90
b = 66.614	β = 90.415
c = 62.926	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	PIXEL	DECTRIS PILATUS 2M		2012-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9796	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.75	35.8	94.9	0.1	0.995	6.4	1.76		55874		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.86	95.3		1.039	0.439	0.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2ves	1.75	35.779	29727	1487	99.515	0.181	0.1784	0.19	0.2234	0.23	25.196

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]
0.375		0.446	-0.842		0.461

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.485
r_dihedral_angle_4_deg	18.511
r_dihedral_angle_3_deg	13.296
r_dihedral_angle_1_deg	7.038
r_lrange_it	5.735
r_lrange_other	5.719
r_scangle_it	4.639
r_scangle_other	4.638
r_scbond_it	3.062
r_scbond_other	3.061
r_mcangle_other	2.745
r_mcangle_it	2.742
r_mcbond_it	1.974
r_mcbond_other	1.966
r_angle_refined_deg	1.628
r_angle_other_deg	1.386
r_nbd_other	0.206
r_nbd_refined	0.202
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_nbd_refined	0.082
r_chiral_restr	0.076
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2296
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing