5TXF | pdb_00005txf

Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in a closed conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4X90Homology Model based on LPLA2 (4x90) generated by MODELLER

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.2 M ammonium formate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.5265.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.887α = 90
b = 123.532β = 96.19
c = 114.778γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-04-17MSINGLE WAVELENGTH
21x-ray100PIXELDECTRIS PILATUS3 6M2014-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97919APS21-ID-D
2SYNCHROTRONAPS BEAMLINE 23-ID-D0.984APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.148.399.60.1760.996.64.148188
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.298.31.2620.5771.14.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHomology Model based on LPLA2 (4x90) generated by MODELLER3.12045564236599.020.25040.249550.260.266510.28RANDOM88.889
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]
3.936.77-5.37-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.526
r_dihedral_angle_3_deg13.873
r_dihedral_angle_4_deg13.03
r_long_range_B_refined6.504
r_long_range_B_other6.504
r_dihedral_angle_1_deg5.921
r_mcangle_other4.023
r_mcangle_it4.022
r_scangle_other3.549
r_mcbond_it2.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.526
r_dihedral_angle_3_deg13.873
r_dihedral_angle_4_deg13.03
r_long_range_B_refined6.504
r_long_range_B_other6.504
r_dihedral_angle_1_deg5.921
r_mcangle_other4.023
r_mcangle_it4.022
r_scangle_other3.549
r_mcbond_it2.295
r_mcbond_other2.293
r_scbond_it1.986
r_scbond_other1.985
r_angle_refined_deg1.318
r_angle_other_deg1.042
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms12156
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms240

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing