6MVD

Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in complex with isopropyl dodec-11-enylfluorophosphonate (IDFP) and a small molecule activator


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TXF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.25 M lithium sulfate, 0.1 M Tris pH 8.5, and 16% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.9368.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.697α = 90
b = 106.377β = 125.45
c = 117.823γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

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
13.13098.90.11511.14.224440
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)
13.13.151000.551.274.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5TXF3.128.820413114587.260.195080.192520.23932RANDOM70.341
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]
-0.42-0.231.1-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_3_deg16.686
r_dihedral_angle_4_deg15.087
r_dihedral_angle_1_deg7.215
r_long_range_B_refined6.294
r_long_range_B_other6.292
r_mcangle_it3.784
r_mcangle_other3.783
r_scangle_other3.664
r_mcbond_it2.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_3_deg16.686
r_dihedral_angle_4_deg15.087
r_dihedral_angle_1_deg7.215
r_long_range_B_refined6.294
r_long_range_B_other6.292
r_mcangle_it3.784
r_mcangle_other3.783
r_scangle_other3.664
r_mcbond_it2.246
r_mcbond_other2.246
r_scbond_it2.137
r_scbond_other2.131
r_angle_refined_deg1.331
r_angle_other_deg0.822
r_chiral_restr0.056
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms5978
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms183

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing