7CID

Crystal structure of P.aeruginosa LpxC in complex with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UHM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529225% PEG 4K 0.2M MgCl2 0.1M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.1241.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.688α = 90
b = 84.225β = 90
c = 93.423γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.4928.36900.1490.9887.349121
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.5686.30.540.8481.93.6

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 REPLACEMENTTHROUGHOUT3UHM2.4928.37860149887.860.20230.200410.23546RANDOM27.023
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]
-2.73-0.22.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.874
r_dihedral_angle_3_deg17.998
r_dihedral_angle_4_deg17.024
r_dihedral_angle_1_deg7.564
r_long_range_B_refined6.427
r_long_range_B_other6.421
r_scangle_other3.563
r_mcangle_it2.761
r_mcangle_other2.761
r_scbond_it2.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.874
r_dihedral_angle_3_deg17.998
r_dihedral_angle_4_deg17.024
r_dihedral_angle_1_deg7.564
r_long_range_B_refined6.427
r_long_range_B_other6.421
r_scangle_other3.563
r_mcangle_it2.761
r_mcangle_other2.761
r_scbond_it2.113
r_scbond_other2.112
r_mcbond_it1.697
r_mcbond_other1.694
r_angle_refined_deg1.537
r_angle_other_deg1.31
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2221
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing