7OJ6

Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DEM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52781.5 M NH4Cl, 0.1 M Na Acetate pH 4.5
Crystal Properties
Matthews coefficientSolvent content
4.0569.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.17α = 90
b = 167.17β = 90
c = 98.37γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9795DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8459.5297.60.0460.0510.0230.99916.62.411434129.032
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)RedundancyNumber Unique Reflections (All)
11.841.8780.80.7180.9210.5640.59311.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5DEM1.8459.52108534579397.560.17240.1710.1975RANDOM45.042
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]
-1.11-1.112.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.145
r_dihedral_angle_4_deg20.533
r_dihedral_angle_3_deg13.792
r_dihedral_angle_1_deg6.858
r_angle_refined_deg2.689
r_angle_other_deg2.132
r_chiral_restr0.177
r_bond_refined_d0.034
r_gen_planes_refined0.017
r_bond_other_d0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.145
r_dihedral_angle_4_deg20.533
r_dihedral_angle_3_deg13.792
r_dihedral_angle_1_deg6.858
r_angle_refined_deg2.689
r_angle_other_deg2.132
r_chiral_restr0.177
r_bond_refined_d0.034
r_gen_planes_refined0.017
r_bond_other_d0.015
r_gen_planes_other0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5922
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
MOLREPphasing