3Q89

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with CDP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch Crystallization	6.8	298	0.1M Bis-Tris (pH 6.8) and 25% PEG mme 2000, Microbatch Crystallization, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.613	α = 90
b = 73.055	β = 108.23
c = 102.272	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	IMAGE PLATE	MAR scanner 345 mm plate	VariMax	2010-05-10	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	2.9	97.14	99.9	0.076	6.9	4.1		29289	1		60.5

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	2.9	3.06	100		0.183	6.4	4	4274

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	2.9	34.19	27487	1473	98.8	0.25422	0.2521	0.29288	RANDOM	35.194

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		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.277
r_dihedral_angle_3_deg	18.067
r_dihedral_angle_4_deg	16.66
r_dihedral_angle_1_deg	6.253
r_scangle_it	2.92
r_scbond_it	1.614
r_angle_refined_deg	1.357
r_mcangle_it	1.013
r_mcbond_it	0.504
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.277
r_dihedral_angle_3_deg	18.067
r_dihedral_angle_4_deg	16.66
r_dihedral_angle_1_deg	6.253
r_scangle_it	2.92
r_scbond_it	1.614
r_angle_refined_deg	1.357
r_mcangle_it	1.013
r_mcbond_it	0.504
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9167
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	52

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.