2ZUA

Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293	100mM HEPES-NaOH, 25% PEG400, 10mM EDTA, pH7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.571	α = 90
b = 73.571	β = 90
c = 214.271	γ = 120

Symmetry
Space Group	P 63

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	ADSC QUANTUM 210		2006-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	2.59	50	95.7	0.084	30.7			20457

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BHN	2.59	47.57	18544	990	95.71	0.22524	0.2218	0.2894	RANDOM	46.978

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]
-0.1	-0.05		-0.1		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.571
r_dihedral_angle_4_deg	25.353
r_dihedral_angle_3_deg	18.473
r_dihedral_angle_1_deg	5.839
r_scangle_it	1.694
r_angle_refined_deg	1.238
r_scbond_it	1.07
r_mcangle_it	0.778
r_mcbond_it	0.449
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.272
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.096
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4894
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

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