3R20

Crystal structure of cytidylate kinase from Mycobacterium smegmatis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	MysmA.00663.a.A1 PS00600 at 37.2 mg/mL against JCSG+ screen condition E2. 0.2 M NaCl, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 215891e2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.22	α = 90
b = 96.22	β = 90
c = 43.15	γ = 120

Symmetry
Space Group	P 3 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	ADSC QUANTUM 315r		2011-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97946	ALS	5.0.1

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	50	98.8	0.072	21.82	7.8	15827	15632		-3	28.667

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	2.05	94.2		0.416	3.94	5.2	1182

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	PDB ENTRY 3R8C	2	50	15571	776	98.39	0.1705	0.1683	0.21	RANDOM	24.2344

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]
-0.94	-0.47		-0.94		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.9
r_dihedral_angle_4_deg	18.829
r_dihedral_angle_3_deg	10.841
r_dihedral_angle_1_deg	4.781
r_scangle_it	3.647
r_scbond_it	2.187
r_angle_refined_deg	1.341
r_mcangle_it	1.212
r_mcbond_it	0.692
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1572
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	19

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction