Experiment: 4CK0

Crystal structure of the integral membrane diacylglycerol kinase - form 2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZE3	PDB ENTRY 3ZE3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.6	277	7-9%(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 coefficient	Solvent content
3.57	65.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.82	α = 90
b = 72.82	β = 90
c = 195.67	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	MARRESEARCH	K-B PAIR OF BIOMORPH MIRRORS	2012-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

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	2.92	60.02	99.1	0.1	9.9	4.8		13563		-3	76.89

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	2.92	3	99.5		0.76	2.5	4.9

Refinement

Statistics
Diffraction ID	Structure Solution 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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3ZE3	2.924	53.006	1.34	13519	644	99.02	0.2495	0.2479	0.2809	0.2924	86.15

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]
12.1579			12.1579		-24.3158

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.559
f_angle_d	0.563
f_chiral_restr	0.031
f_bond_d	0.012
f_plane_restr	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2555
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	83

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing