4EHY

Crystal structure of LpxK from Aquifex aeolicus in complex with ADP/Mg2+ at 2.2 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EHXPDB ENTRY 4EHX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop, vapor diffusion7.5293The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained 20% seed stock, ~1 mg/ml protein, 48% MPD, 80 mM Hepes pH 7.5, 4 mM Hepes pH 8.0, 130 mM NaCl, 3.4% glycerol, ~0.06% DDM, 1.8 mM ATP, 1.8 mM MgCl2, sutting drop, vapor diffusion, temperature 293K, sitting drop, vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
3.564.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.11α = 90
b = 75.61β = 90
c = 104.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00APS22-BM

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
12.19950980.04913.64.7268212628522
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)
12.1992.2486.90.4343.61151

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4EHX2.19928.4010.082628524602199991.730.18080.17790.213265.3908
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]
-0.284311.4845-11.2002
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.299
f_angle_d1.157
f_chiral_restr0.073
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2520
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms47

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling