6PT8 | pdb_00006pt8

Crystal Structure of CobT from Methanocaldococcus jannaschii in complex with Adenine Alpha-Ribotide and Nicotinic Acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	Crystals formed by mixing 1:1 ratio of 13.3 mg/mL protein solution with well solution containing 100 mM 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (HEPPS) pH 8.5 and 22% (w/v) PEG 8K. 1 mM adenine and 50 mM Sodium/Potassium Phosphate pH 7.0 were added to protein prior to mixing with well solution. Substrates were captured in lattice prior to freezing by soaking crystals in 20% (w/v) ethylene glycol, 100 mM HEPPS pH 8.5, 22% (w/v) PEG 8K, 25 mM sodium/potassium phosophate pH 7.0, 1 mM nicotinic acid mononucleotide, and 1 mM adenine for 30 minutes. Crystals were then soaked in the same solution, but with 30% PEG 8K instead of 20% ethylene glycol and 20% PEG 8K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.39	α = 90
b = 138.64	β = 108.32
c = 51.15	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	PIXEL	DECTRIS PILATUS3 X 6M		2018-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

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	1.4	41.973	98.95	0.09626	12.18	6.8		118689

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	1.4	1.45	98.98		0.6674	2.92	6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3L0Z	1.4	41.973	1.36	118680	5933	98.85	0.1542	0.1531	0.1748	18.8823

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5307
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms	106

Software

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

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.