2QVL

Crystal Structure of Diacylglycerol Kinase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	drop: 0.1 M Tris pH 8.5, 9% PEG2KMME; well: 0.1 M Tris pH 8.5, 18% PEG2KMME, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.21	α = 90
b = 124.21	β = 90
c = 48.502	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	170	CCD	MARMOSAIC 300 mm CCD	mirrors	2007-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9794	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	26.15	99.8	0.094	28.1	8.8	15527	15472

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)
	2.4	2.49	99.5		0.376	8.2	6.1	1491

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.4	26.15	15601	14042	730	94.69	0.23087	0.22869	0.27213	RANDOM	39.969

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.432
r_dihedral_angle_3_deg	18.402
r_dihedral_angle_4_deg	16.672
r_dihedral_angle_1_deg	6.828
r_scangle_it	3.44
r_scbond_it	2.269
r_mcangle_it	1.336
r_angle_refined_deg	1.335
r_mcbond_it	1.111
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.172
r_symmetry_hbond_refined	0.161
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2171
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing