3PNQ | pdb_00003pnq

Crystal Structure of E.coli Dha kinase DhaK (H56N) complex with Dha

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	295	20% PEG 8000, 0.1M sodium citrate pH 5.6, vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.232	α = 90
b = 101.073	β = 89.95
c = 99.349	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			2010-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

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	2.2	49.67	99.3	0.086	8.3	3.7		81917

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)
	2.2	2.28	98.4		0.205		3.6	8077

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	49.67	81897	4149	98.98	0.2005	0.1995	0.1982	0.2196	0.2192	RANDOM	20.7449

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]
-12.77		3.71	31.8		-19.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.764
r_dihedral_angle_4_deg	15.918
r_dihedral_angle_3_deg	14.817
r_dihedral_angle_1_deg	6.312
r_scangle_it	3.34
r_scbond_it	2.045
r_angle_refined_deg	1.433
r_mcangle_it	1.313
r_mcbond_it	0.719
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10100
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing