Experiment: 4CJZ

Crystal structure of the integral membrane diacylglycerol kinase DgkA- 9.9, delta 4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZE5	PDB ENTRY 3ZE5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.6	277	7-8 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 2-4 %(V/V) 1,4-BUTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 9.9 MONOACYLGLYCEROL (9.9 MAG, MONOOLEIN) AS THE HOSTING LIPID.

Crystal Properties
Matthews coefficient	Solvent content
4.14	70.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.78	α = 90
b = 72.78	β = 90
c = 199.28	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	2011-07-21	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	3.25	53.27	99.6	0.12	12.7	9.7		10196		-3	108.82

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	3.25	3.33	99.8		1.15	2.1	10

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3ZE5	3.25	53.267	1.37	10166	475	99.47	0.2573	0.2554	0.2635	0.2915	0.2947	142.58

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	9.905
f_angle_d	0.405
f_chiral_restr	0.028
f_bond_d	0.002
f_plane_restr	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2571
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	25

Software

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