8QKA

Structure of K. pneumoniae LpxH in complex with JEDI-852


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUNPUBLISHED MODEL FROM THIS LAB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5293Morpheus III G12 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 3 8.5 50 % Precipitant Mix 4
Crystal Properties
Matthews coefficientSolvent content
2.6353.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.013α = 90
b = 60.013β = 90
c = 284.658γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.918401MAX IVBioMAX

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
12301000.1090.1120.0240.99918.23621782
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.050.7520.7710.1770.985.4

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 REPLACEMENTTHROUGHOUT229.3820615105499.920.221140.219020.26351RANDOM39.865
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]
0.480.240.48-1.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.107
r_long_range_B_other8.269
r_long_range_B_refined8.222
r_dihedral_angle_2_deg7.76
r_dihedral_angle_1_deg7.225
r_scangle_other6.316
r_mcangle_it5.169
r_mcangle_other5.169
r_scbond_other4.46
r_scbond_it4.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.107
r_long_range_B_other8.269
r_long_range_B_refined8.222
r_dihedral_angle_2_deg7.76
r_dihedral_angle_1_deg7.225
r_scangle_other6.316
r_mcangle_it5.169
r_mcangle_other5.169
r_scbond_other4.46
r_scbond_it4.44
r_mcbond_it3.967
r_mcbond_other3.965
r_angle_refined_deg1.506
r_angle_other_deg0.5
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms1836
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing