4CK0

Crystal structure of the integral membrane diacylglycerol kinase - form 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZE3PDB ENTRY 3ZE3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.62777-9%(V/V) 2-METHYL-2-4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREE CELSIUS WITH THE MONOOLEIN AS THE HOSTING LIPID. CRYSTALS WERE SOAKED AT 4 DEGREE CELSIUS WITH 10 MM AMPPCP AND 60 MM MAGNESIUM IN THE CRYSTALLIZATION CONDITION FOR 2 H BEFORE HARVESTING.
Crystal Properties
Matthews coefficientSolvent content
3.5765.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.82α = 90
b = 72.82β = 90
c = 195.67γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHK-B PAIR OF BIOMORPH MIRRORS2012-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.9260.0299.10.19.94.813563-376.89
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92399.50.762.54.9

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 3ZE32.92453.0061.341351964499.020.24950.24790.280986.15
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]
12.157912.1579-24.3158
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.559
f_angle_d0.563
f_chiral_restr0.031
f_bond_d0.012
f_plane_restr0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2555
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms83

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing