Experiment: 6IG2

Structure of mitochondrial CDP-DAG synthase Tam41 complexed with CTP, delta 74, F240A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IG4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION, RECRYSTALLIZATION		289.15	0.1 M HEPES-Na, pH 7.5, 9% Tacsimate, pH 7.0, 2% PEG 3350, incubated with 10 mM MgCl2, 5 mM CTP for 1 h before crystallization

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.266	α = 90
b = 187.418	β = 90
c = 186.57	γ = 90

Symmetry
Space Group	P 21 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173.15	PIXEL	DECTRIS PILATUS3 6M		2017-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.977	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.88	50	100	0.042	20.7	6.5		44684

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	100		0.482	1.9	6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6IG4	2.882	47.604	1.34	42315	2135	94.2	0.2185	0.2164	0.2153	0.2588	0.2572	Random selection

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	24.803
f_angle_d	0.477
f_chiral_restr	0.04
f_plane_restr	0.003
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8946
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	29

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing