2AZ3 | pdb_00002az3

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum in complex with CDP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.2M MgCl2, 0.1M HEPES-Na, pH7.5, 30% PEG 400, 10mM Co(NH3)6Cl3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.37	α = 90
b = 71.52	β = 95.53
c = 157.99	γ = 90

Symmetry
Space Group	C 1 2 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	MARRESEARCH		2005-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	20	80.3	0.063	10.14	2.7	70403	56525			45.36

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	2.3	64.9		0.289	3.32

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1nue	2.2	20	53700	53700	2824	80.43	0.2032	0.2032	0.19964	0.21	0.27074	0.2	RANDOM	37.966

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]
-0.09		-0.29	0.59		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.651
r_scangle_it	4.064
r_scbond_it	2.542
r_angle_refined_deg	1.934
r_mcangle_it	1.605
r_angle_other_deg	0.977
r_mcbond_it	0.896
r_symmetry_vdw_other	0.325
r_nbd_other	0.25
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.185
r_symmetry_hbond_refined	0.176
r_chiral_restr	0.113
r_nbtor_other	0.096
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10750
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	227

Software

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