7CI7

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 DIFFUSION8.52930.03M Diethylene glycol 0.03M Triethylene glycol 0.03M Tetraethylene glycol 0.03M Pentaethylene glycol 0.1M Tris - BICINE pH 8.5 20 % v/v PEG 500 MME 10 % w/v PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.2846.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.716α = 90
b = 67.046β = 90.96
c = 63.258γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2020-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54056

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.122.1799.90.1945.924.717500
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.181000.5611.674.7

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 REPLACEMENTTHROUGHOUT3UHM2.122.171651795799.790.196890.193880.24964RANDOM23.751
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]
0.060.01-0.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.241
r_dihedral_angle_3_deg15.383
r_dihedral_angle_4_deg15.354
r_dihedral_angle_1_deg7.508
r_long_range_B_refined7.069
r_long_range_B_other7.067
r_scangle_other3.757
r_mcangle_it2.929
r_mcangle_other2.928
r_scbond_it2.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.241
r_dihedral_angle_3_deg15.383
r_dihedral_angle_4_deg15.354
r_dihedral_angle_1_deg7.508
r_long_range_B_refined7.069
r_long_range_B_other7.067
r_scangle_other3.757
r_mcangle_it2.929
r_mcangle_other2.928
r_scbond_it2.316
r_scbond_other2.315
r_mcbond_it1.828
r_mcbond_other1.827
r_angle_refined_deg1.663
r_angle_other_deg1.339
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2301
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing