8RQR

In meso structure of apolipoprotein N-acyltransferase, Lnt, from Escherichia coli in 7.10 monoacylglycerol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7ACI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293100 mM MES pH 6.0, 8 %(v/v) MPD, and 50-400 mM sodium or potassium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.4750.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.679α = 90
b = 76.461β = 90
c = 157.08γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X CdTe 9M2021-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
12.1946.599.10.997.76.43088133.28
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)
12.192.270.31

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.1946.51.3330740154099.010.20090.19850.245839.62
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.428
f_angle_d0.7979
f_chiral_restr0.0441
f_plane_restr0.0091
f_bond_d0.0043
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4026
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms216

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing