6WMV

Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii with evidence of substrate binding

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D91	5D91,4O6M
experimental model	PDB	4O6M	5D91,4O6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6.1	295	100 mM NaCl, 100 mM Sodium Citrate, pH 6.1, 40 mM MgCl2, 29% PEG 400, 500 uM L-myo-inositol-1-phosphate (prepared in house), 2.5 mM CDP (Sigma) (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein at a 1:1.5 protein to lipid ratio

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.089	α = 90
b = 60.857	β = 90.74
c = 85.417	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	PIXEL	DECTRIS EIGER X 16M	MD2 diffractometer	2018-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.142	78.083	58.72	0.07329	0.1036	0.07329	0.995	9.78	2		26006			41.06

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.142	2.221	1.57		0.4034	0.5705	0.4034	0.594	1.73	2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5D91,4O6M	2.142	78.083	1.37	25995	1297	58.53	0.2252	0.2228	0.2695	45.381

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5013
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	268

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
STARANISO	data scaling
PARROT	phasing
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.