3Q86

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with GTP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch Crystallization	5	298	0.1M Mgacetate, 0.1M citric acid, pH 5, 14% PEG 8000 , Microbatch Crystallization, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.302	α = 90
b = 75.302	β = 90
c = 154.712	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	Goebel Mirrors	2010-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

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	2.36	37.65	96.8	0.03	46.4	7.6		13104	1		29.3

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	2.36	2.48	78.5		0.081	20.4	7	1550

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	3Q83	2.38	37.65	12456	644	99.54	0.16877	0.16626	0.22011	RANDOM	19.665

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.888
r_dihedral_angle_4_deg	25.788
r_dihedral_angle_3_deg	16.842
r_dihedral_angle_1_deg	6.983
r_scangle_it	4.678
r_scbond_it	2.782
r_angle_refined_deg	1.926
r_mcangle_it	1.555
r_mcbond_it	0.794
r_chiral_restr	0.126
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2290
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	66

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling