5AE2

Ether Lipid-Generating Enzyme AGPS in complex with inhibitor 1e

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BBY	PDB ENTRY 4BBY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.53	α = 90.57
b = 98.57	β = 90.14
c = 107.07	γ = 95.67

Symmetry
Space Group	P 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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23		ESRF	ID23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2	72.7	85.4	0.14	6.4	4		142107

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	82.6		0.92	1.7	4

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	PDB ENTRY 4BBY	2	107.06	140546	1516	85.3	0.17556	0.17501	0.22882	RANDOM	27.515

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]
-0.59	0.41	-0.9	0.09	-1.12	0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.665
r_dihedral_angle_4_deg	16.958
r_dihedral_angle_3_deg	16.671
r_dihedral_angle_1_deg	6.797
r_mcangle_it	3.196
r_scbond_it	3.112
r_mcbond_it	2.161
r_mcbond_other	2.157
r_angle_refined_deg	1.909
r_angle_other_deg	1.1
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17472
Nucleic Acid Atoms
Solvent Atoms	993
Heterogen Atoms	328

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing