3Q8Y

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP and Vanadate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch Crystallization	8.5	298	0.1M Tris-Cl (pH 8.5), 20% PEG 3350, Microbatch Crystallization, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.91	α = 90
b = 71.367	β = 108.04
c = 160.08	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	MARMOSAIC 225 mm CCD	Grazing angle 2.8 mrad	2010-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.73550	ESRF	BM14

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	2.7	60.49	100	0.15	5.6	4.1		35635	1		67.6

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	2.7	2.85	100		0.462	2.1	4.1	5175

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	2.7	51.67	33709	1777	99.61	0.25181	0.25077	0.27077	RANDOM	64.821

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	0.03		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.319
r_dihedral_angle_4_deg	22.13
r_dihedral_angle_3_deg	17.531
r_dihedral_angle_1_deg	6.073
r_scangle_it	2.846
r_scbond_it	1.612
r_angle_refined_deg	1.417
r_mcangle_it	1.089
r_mcbond_it	0.551
r_chiral_restr	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.319
r_dihedral_angle_4_deg	22.13
r_dihedral_angle_3_deg	17.531
r_dihedral_angle_1_deg	6.073
r_scangle_it	2.846
r_scbond_it	1.612
r_angle_refined_deg	1.417
r_mcangle_it	1.089
r_mcbond_it	0.551
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9232
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	206

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.