8QK5

Structure of K. pneumoniae LpxH in complex with EBL-3647


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherOtherUnpublised model from ths lab

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5293Morpheus III - G11 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 3 8.5 50 % Precipitant Mix 3
Crystal Properties
Matthews coefficientSolvent content
2.7154.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.418α = 90
b = 60.418β = 90
c = 287.692γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965459ESRFMASSIF-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
11.953099.90.99912.57.723964
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)
11.9520.652

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 REPLACEMENTTHROUGHOUT1.9529.6522624121999.780.241950.239730.28192RANDOM48.005
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]
0.770.380.77-2.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.209
r_long_range_B_refined7.618
r_long_range_B_other7.566
r_dihedral_angle_1_deg6.892
r_dihedral_angle_2_deg6.54
r_scangle_other5.965
r_mcangle_it5.433
r_mcangle_other5.431
r_scbond_it4.452
r_scbond_other4.425
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.209
r_long_range_B_refined7.618
r_long_range_B_other7.566
r_dihedral_angle_1_deg6.892
r_dihedral_angle_2_deg6.54
r_scangle_other5.965
r_mcangle_it5.433
r_mcangle_other5.431
r_scbond_it4.452
r_scbond_other4.425
r_mcbond_it4.255
r_mcbond_other4.25
r_angle_refined_deg1.335
r_angle_other_deg0.466
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms1844
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing