4DIE

Crystal structure of a cytidylate kinase CmK from Mycobacterium abscessus bound to cytidine-5'-monophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R8C	pdb entry 3R8C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	MyabA.00663.a.A1 PW30208 at 27.9 mg/mL with 4 mM C5P and 4 mM ADP against JCSG+ screen condition E1, 0.1 M sodium cacodylate pH 6.5, 1 M trisodium citrate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220703e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.76	α = 90
b = 96.52	β = 97.22
c = 78.79	γ = 90

Symmetry
Space Group	P 1 21 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		2011-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976	ALS	5.0.3

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	2.65	50	98.6	0.086	16.56	4.3	30667	30247		-3	42.885

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	2.65	2.72	98.2		0.541	3.07

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3R8C	2.65	50	30247	1520	98.64	0.233	0.231	0.23	0.27	0.27	RANDOM	39.0239

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]
-3.02		-0.08	-0.66		3.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.981
r_dihedral_angle_4_deg	21.774
r_dihedral_angle_3_deg	13.607
r_dihedral_angle_1_deg	4.997
r_angle_refined_deg	1.472
r_angle_other_deg	1.182
r_chiral_restr	0.068
r_bond_refined_d	0.01
r_bond_other_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5758
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	104

Software

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

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 R01GM157729.