8QK2

Structure of K.pneumoniae LpxH in complex with EBL-3339


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5293Morpheus III screen, G6 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 2 7.5 50 % Precipitant Mix 2
Crystal Properties
Matthews coefficientSolvent content
2.3254.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.204α = 90
b = 60.204β = 90
c = 286.779γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976254DiamondI03

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
11.953088.50.090.0940.0280.99920.5202111436.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9521.6720.5070.792

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 REPLACEMENTTHROUGHOUT1.9529.9619918108288.680.225060.223540.25271RANDOM39.787
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]
0.760.380.76-2.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.705
r_dihedral_angle_1_deg6.433
r_dihedral_angle_2_deg6.38
r_long_range_B_refined5.67
r_long_range_B_other5.586
r_scangle_other4.23
r_mcangle_it3.776
r_mcangle_other3.775
r_scbond_other2.823
r_scbond_it2.815
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.705
r_dihedral_angle_1_deg6.433
r_dihedral_angle_2_deg6.38
r_long_range_B_refined5.67
r_long_range_B_other5.586
r_scangle_other4.23
r_mcangle_it3.776
r_mcangle_other3.775
r_scbond_other2.823
r_scbond_it2.815
r_mcbond_it2.686
r_mcbond_other2.686
r_angle_refined_deg1.199
r_angle_other_deg0.426
r_chiral_restr0.065
r_bond_refined_d0.007
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 Atoms1850
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
REFMACphasing