5TXF

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X90	Homology Model based on LPLA2 (4x90) generated by MODELLER

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.2 M ammonium formate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.09

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2014-04-17	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2014-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97919	APS	21-ID-D
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.984	APS	23-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.1	48.3	99.6	0.176	0.99	6.6	4.1		48188

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)	Redundancy	Number Unique Reflections (All)
1	3.1	3.2	98.3		1.262	0.577	1.1	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Homology Model based on LPLA2 (4x90) generated by MODELLER	3.1	20	45564	2365	99.02	0.2504	0.24955	0.26651	RANDOM	88.889

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]
3.93		6.77	-5.37		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.526
r_dihedral_angle_3_deg	13.873
r_dihedral_angle_4_deg	13.03
r_long_range_B_refined	6.504
r_long_range_B_other	6.504
r_dihedral_angle_1_deg	5.921
r_mcangle_other	4.023
r_mcangle_it	4.022
r_scangle_other	3.549
r_mcbond_it	2.295
r_mcbond_other	2.293
r_scbond_it	1.986
r_scbond_other	1.985
r_angle_refined_deg	1.318
r_angle_other_deg	1.042
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
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 Atoms	Number
Protein Atoms	12156
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	240

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
Aimless	data scaling
PHASER	phasing