7OJP | pdb_00007ojp

Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DEM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	278	1.6 M (NH4)2SO4, 10% 1,4-Dioxane, 0.1 M MES pH 6.7

Crystal Properties
Matthews coefficient	Solvent content
4.93	75.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 245.627	α = 90
b = 367.548	β = 90
c = 370.677	γ = 90

Symmetry
Space Group	C 2 2 21

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 6M		2018-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim 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	2.84	105.72	99.5	0.33	0.127	0.982	5.7	6.7		386908			39.403

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.84	2.89	89.8		2.295	0.898	0.445	1	6.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5DEM	2.84	105.72	367331	19383	99.46	0.2039	0.2032	0.21	0.2163	0.22	RANDOM	49.708

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]
2.08			-1.24		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.521
r_dihedral_angle_4_deg	21.33
r_dihedral_angle_3_deg	19.412
r_dihedral_angle_1_deg	7.149
r_angle_refined_deg	1.759
r_angle_other_deg	1
r_chiral_restr	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.521
r_dihedral_angle_4_deg	21.33
r_dihedral_angle_3_deg	19.412
r_dihedral_angle_1_deg	7.149
r_angle_refined_deg	1.759
r_angle_other_deg	1
r_chiral_restr	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	59184
Nucleic Acid Atoms
Solvent Atoms	422
Heterogen Atoms	871

Software

Software
Software Name	Purpose
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.