2AZ1

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NUE	PDB ENTRY 1NUE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.2M CaCl2, 0.1M HEPES-Na, pH 7.5, 28% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.28	α = 90
b = 108.7	β = 90
c = 119.65	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	2.3	20	99.1	0.09	9.31	2.9	40870	40514			54.98

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)
	2.3	2.44	97.2		0.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NUE	2.35	20	36370	36283	1918	99.76	0.22035	0.22035	0.21668	0.28944	RANDOM	47.772

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]
1.96			1.63		-3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.428
r_scangle_it	3.811
r_scbond_it	2.351
r_angle_refined_deg	1.776
r_mcangle_it	1.527
r_angle_other_deg	0.977
r_mcbond_it	0.84
r_symmetry_hbond_refined	0.326
r_symmetry_vdw_refined	0.307
r_xyhbond_nbd_refined	0.254
r_nbd_other	0.247
r_nbd_refined	0.227
r_symmetry_vdw_other	0.203
r_metal_ion_refined	0.154
r_chiral_restr	0.106
r_nbtor_other	0.095
r_bond_refined_d	0.021
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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	7094
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing