5KTN

Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound dihydroxyacetone phosphate (DHAP) and Fe4S4 cluster

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		296	210 mM ammonium chloride, 8 - 15% polyethylene glycol 4000, and 40 mM HEPES, pH 5.5 - 7.5. DHAP was added to the protein solution to a final concentration of 7-10 mM

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.303	α = 90
b = 52.522	β = 112.2
c = 55.544	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 315		2013-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97925	APS	24-ID-E

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	1.34	35	99.4	0.047	19.3	3.6		56267

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	1.34	1.39	95.1		0.242	5	2.8

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Crystal structure of Pyrococcus horikoshii NadA with bound malate and lacking Fe4S4 cluster (PDB entry 1WZU)	1.34	33.636	1.36	56248	2850	99.28	0.1243	0.1227	0.1546

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.151
f_angle_d	1.728
f_chiral_restr	0.084
f_bond_d	0.012
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2419
Nucleic Acid Atoms
Solvent Atoms	522
Heterogen Atoms	21

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
HKL-2000	data reduction
HKL-2000	data scaling

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 R01GM133198.