6I49 | pdb_00006i49

Structure of P. aeruginosa LpxC with compound 17a: (2R)-N-Hydroxy-2-methyl-2-(methylsulfonyl)-4(6((4(morpholinomethyl)phenyl)ethynyl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)yl)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	0.2 M ammonium acetate, 0.1 M sodium acetate pH 4.6, 7 % (w/v) PEG 400, 7 % (w/v) PEG 500 MME, 7 % (w/v) PEG 600, 7 % (w/v) PEG 1000, 5 % (v/v) ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.313	α = 90
b = 89.178	β = 90
c = 35.383	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 2M-F		2017-10-01	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	1.94	43.122	97.9	0.109	0.995	8.7	3.62		74154		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	2.06	96.4		0.725	2.1

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	1.94	43.122	39617	1982	98.186	0.186	0.1832	0.19	0.2429	0.24	24.151

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]
0.851			0.025		-0.877

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.557
r_dihedral_angle_4_deg	20.678
r_dihedral_angle_3_deg	14.384
r_dihedral_angle_1_deg	7.417
r_lrange_other	6.898
r_lrange_it	6.869
r_scangle_it	6.115
r_scangle_other	6.114
r_scbond_it	4.418
r_scbond_other	4.417
r_mcangle_it	3.93
r_mcangle_other	3.929
r_mcbond_it	3.185
r_mcbond_other	3.171
r_angle_refined_deg	2.417
r_angle_other_deg	1.619
r_symmetry_nbd_refined	0.276
r_nbd_other	0.23
r_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.147
r_ncsr_local_group_1	0.12
r_chiral_restr	0.111
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_other	0.065
r_bond_refined_d	0.021
r_gen_planes_refined	0.013
r_xyhbond_nbd_other	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	4545
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	68

Software

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