2GRJ

Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase) (tm1387) from THERMOTOGA MARITIMA at 2.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	5.2	293	30.0M NaCl, 32.5% PEG-8000, 0.1M Na,K-Phosphate pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.832	α = 90
b = 87.217	β = 106.92
c = 98.586	γ = 90

Symmetry
Space Group	P 1 21 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	MAR CCD 165 mm		2003-07-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.97921, 0.9537246, 0.97907	APS	14-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	2.6	47.7	96.8	0.07	7.79	3.37		44701			40.15

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	2.6	2.69		74.7	0.375	1.84

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.6	25.29	44609	2249	98.41	0.193	0.19328	0.191	0.245	RANDOM	35.699

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]
0.66		1.01	-1.92		1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.132
r_dihedral_angle_3_deg	16.457
r_dihedral_angle_4_deg	15.29
r_scangle_it	6.649
r_dihedral_angle_1_deg	5.622
r_scbond_it	4.645
r_mcangle_it	2.158
r_angle_refined_deg	1.791
r_mcbond_it	1.742
r_angle_other_deg	0.899
r_mcbond_other	0.251
r_nbd_refined	0.229
r_symmetry_hbond_refined	0.186
r_nbd_other	0.177
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.158
r_symmetry_vdw_other	0.14
r_xyhbond_nbd_refined	0.133
r_nbtor_other	0.088
r_chiral_restr	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10846
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	572

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing