6WM5

Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5D915D91,4O6M
experimental modelPDB 4O6M5D91,4O6M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE6295100 mM Sodium citrate, pH 6, 50 mM sodium chloride, 20 mM magnesium chloride hexahydrate, 22% PEG 400 (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein (Sigma) in a 1:1.5 protein to lipid ratio (w/w). Monoolein was doped with 2% CDP-DAG
Crystal Properties
Matthews coefficientSolvent content
2.550.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.338α = 90
b = 60.241β = 90.91
c = 85.377γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16MMD2 diffractometer2017-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9791APS24-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9649.22660.10610.15010.10610.9896.231.93748225.57
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)RedundancyNumber Unique Reflections (All)
11.962.0373.270.640.90510.640.110.98

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5D91,4O6M1.96149.221.3337478193065.380.23690.23470.27733.7529
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 AtomsNumber
Protein Atoms5025
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms460

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling
PARROTphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction