8QJZ

Crystal structure of E. coli LpxH in complex with lipid X


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherunpublished model from this lab

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5293Morpheus III (G7) 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 2 7.5 50 % Precipitant Mix 3
Crystal Properties
Matthews coefficientSolvent content
2.9758.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.827α = 90
b = 81.392β = 100.32
c = 33.127γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-Fquasi-periodic elliptically polarizing undulator (qEPU)2019-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91589DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.3567.6990.99911.16.170366
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.420.827

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.353066887346899.170.172240.171460.18733RANDOM16.599
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]
0.16-1.41.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.817
r_dihedral_angle_2_deg7.337
r_dihedral_angle_1_deg5.782
r_long_range_B_refined4.327
r_long_range_B_other4.139
r_scangle_other2.933
r_scbond_it1.968
r_scbond_other1.945
r_mcangle_it1.837
r_mcangle_other1.837
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.817
r_dihedral_angle_2_deg7.337
r_dihedral_angle_1_deg5.782
r_long_range_B_refined4.327
r_long_range_B_other4.139
r_scangle_other2.933
r_scbond_it1.968
r_scbond_other1.945
r_mcangle_it1.837
r_mcangle_other1.837
r_angle_refined_deg1.281
r_mcbond_it1.19
r_mcbond_other1.173
r_angle_other_deg0.465
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms1901
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing