3Q3L

The neutron crystallographic structure of inorganic pyrophosphatase from Thermococcus thioreducens

NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	counter diffusion, free-interface diffusion	6.5	298	Calcium Chloride, MPD, pH 6.5, counter diffusion, free-interface diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.1	α = 90
b = 95.51	β = 98.08
c = 113.726	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	298	IMAGE PLATE	LADI-III		2010-07-19		LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	LANSCE BEAMLINE PCS	1 - 2.5	LANSCE	PCS

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	2.5	37.53	73.7	0.146			38788	28587		2

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	2.5	2.64	58.7		0.177	5.4	3.4

Refinement

Statistics
Diffraction ID	Structure Solution 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
NEUTRON DIFFRACTION	REFINEMENT AGAINST FIXED MODEL	3I98	2.5	36.418	0.06	28530	1425	73.13	0.2233	0.221	0.268

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]
-10.8628		-0.7737	-6.4316		-7.9679

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.329
f_angle_d	2.41
f_bond_d	0.099
f_chiral_restr	0.076
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8568
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
LAUEGEN	data collection
LAUEGEN	data reduction
LAUESCALE	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.