2VES

Crystal Structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		PALPXC, 10 MG/ML IN 25 MM HEPES PH 7.0, 2 MM TCEP, 0.3 M NACL, 1MM ZNCL2. BB-78485 ADDED TO 1 MM. HANGING DROP, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M AMMONIUM SULFATE AND 10 % PEG 8000, 10 MM ZNCL2.

Crystal Properties
Matthews coefficient	Solvent content
2.13	50.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.542	α = 90
b = 103.331	β = 90
c = 105.284	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	CCD	ADSC CCD	MIRRORS	2004-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	34.15	99.9	0.08	23.61	6.4		78112

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	1.97	99.5		0.52	2.5	5.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1P42	1.9	73.72	74089	3927	99.6	0.179	0.177	0.221	RANDOM	23.05

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]
0.75			-0.83		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.124
r_dihedral_angle_4_deg	15.259
r_dihedral_angle_3_deg	12.611
r_dihedral_angle_1_deg	5.822
r_scangle_it	1.856
r_scbond_it	1.289
r_angle_refined_deg	1.122
r_angle_other_deg	1.024
r_mcangle_it	0.768
r_mcbond_it	0.67
r_symmetry_vdw_other	0.262
r_nbd_refined	0.196
r_nbtor_refined	0.172
r_nbd_other	0.168
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.101
r_nbtor_other	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6863
Nucleic Acid Atoms
Solvent Atoms	1223
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing