7OKB | pdb_00007okb

Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 45

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
5.53	77.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 378.61	α = 90
b = 378.61	β = 90
c = 264.64	γ = 90

Symmetry
Space Group	P 42 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 EIGER2 X 16M		2019-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.58	109.08	100	0.615	0.626	0.118	0.994	7.3	27.8		223901			95.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.58	3.67	100		3.469	3.53	0.654	0.592		29

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	3.58	109.08	212833	10979	99.98	0.1954	0.1945	0.2	0.2122	0.21	RANDOM	95.596

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]
-0.36			-0.36		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.642
r_dihedral_angle_4_deg	21.531
r_dihedral_angle_3_deg	21.4
r_dihedral_angle_1_deg	9.124
r_angle_refined_deg	2.287
r_angle_other_deg	1.385
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.642
r_dihedral_angle_4_deg	21.531
r_dihedral_angle_3_deg	21.4
r_dihedral_angle_1_deg	9.124
r_angle_refined_deg	2.287
r_angle_other_deg	1.385
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	59100
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	1106

Software

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

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.