2QV7

Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	drop: 0.1 M Tris pH 8.5, 9% PEG2K MME; well: 0.1 M Tris pH 8.5, 18% PEG2K MME, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.76	α = 90
b = 123.76	β = 90
c = 47.68	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	2007-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	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	2.3	30	99.8	0.128	24.5	12.2	17025	16997

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	2.3	2.38	99.8		0.431	4.2	8.3	1667

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	Rigid body refinement of DgkB	THROUGHOUT	2.3	29.17	16997	16069	857	99.58	0.20845	0.20648	0.2464	RANDOM	34.138

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.929
r_dihedral_angle_4_deg	17.523
r_dihedral_angle_3_deg	14.053
r_dihedral_angle_1_deg	5.887
r_scangle_it	1.603
r_angle_refined_deg	1.122
r_scbond_it	1.093
r_mcangle_it	0.676
r_mcbond_it	0.43
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.189
r_nbd_refined	0.177
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.107
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2324
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	28

Software

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