3Q8U

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch Crystallization	6.5	298	0.1M Bis-Tris, 6.5, 25% PEG 2000, Microbatch Crystallization, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.27	α = 90
b = 103.065	β = 90
c = 127	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	IMAGE PLATE	MAR scanner 345 mm plate	VariMax	2010-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	2.21	34.52	97.4	0.05	16.1	3.4		44437	1		22.4

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	2.21	2.33	89.2		0.208	5.6	3.2	5870

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	2.22	34.52	42078	2230	97.82	0.18389	0.18008	0.25846	RANDOM	18.436

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.428
r_dihedral_angle_4_deg	21.805
r_dihedral_angle_3_deg	16.884
r_dihedral_angle_1_deg	6.926
r_scangle_it	4.296
r_scbond_it	2.806
r_angle_refined_deg	2
r_mcangle_it	1.587
r_mcbond_it	0.853
r_chiral_restr	0.137
r_bond_refined_d	0.021
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6958
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms	167

Software

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