6I47 | pdb_00006i47

Structure of P. aeruginosa LpxC with compound 10: (2RS)-4-(5-(2-Fluoro-4-methoxyphenyl)-1-oxoisoindolin-2-yl)-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide

X-RAY DIFFRACTION

---

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
2.31	46.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.279	α = 90
b = 66.503	β = 90.76
c = 63.452	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		2015-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	45.906	91.1	0.095	0.994	6.6	1.86		42579		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.01			0.732	0.405

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	1.9	45.906	23703	1185	99.317	0.206	0.2032	0.21	0.2579	0.26	27.44

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]
1.137		0.552	-0.413		-0.738

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.839
r_dihedral_angle_4_deg	16.998
r_dihedral_angle_1_deg	16.748
r_dihedral_angle_3_deg	14.872
r_lrange_it	5.71
r_lrange_other	5.609
r_scangle_it	3.568
r_scangle_other	3.567
r_mcangle_other	3.277
r_mcangle_it	3.274
r_scbond_it	2.265
r_scbond_other	2.264
r_mcbond_it	2.065
r_mcbond_other	2.065
r_angle_refined_deg	1.637
r_angle_other_deg	1.317
r_symmetry_nbd_refined	0.27
r_nbd_refined	0.192
r_nbd_other	0.182
r_symmetry_nbd_other	0.18
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2286
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	32

Software

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