3S55

Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OEC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	MyabA.01326.f.A1 PW30378 at 27.3 mg/mL against JCSG+ screen condition D10, 0.2 M Ca(OAc)2, 0.1 M Na cacodylate pH 6.5, 40% PEG 300, direct cryo, crsytal tracking ID 219629d10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.36	α = 81.77
b = 84.97	β = 76.78
c = 100.89	γ = 74.23

Symmetry
Space Group	P 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	RIGAKU SATURN 944+		2011-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.1	50	94.9	0.104	11.14	3.9	125503	119101		-3	18.864

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	2.1	2.15	89.3		0.249	5.59	3.6	9192

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	3oec	2.1	50	119100	5974	94.95	0.1917	0.1893	0.19	0.237	0.2	RANDOM	12.2523

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]
-0.34	-0.18	-0.39	0.4	0.38	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.07
r_dihedral_angle_4_deg	15.913
r_dihedral_angle_3_deg	13.639
r_dihedral_angle_1_deg	6.163
r_scangle_it	3.008
r_scbond_it	1.902
r_angle_refined_deg	1.484
r_mcangle_it	1.1
r_mcbond_it	0.628
r_chiral_restr	0.093

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15649
Nucleic Acid Atoms
Solvent Atoms	1254
Heterogen Atoms	360

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
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.