3Q3L | pdb_00003q3l

The neutron crystallographic structure of inorganic pyrophosphatase from Thermococcus thioreducens

NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I98

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		2010-07-20		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 (Depositor)	R-Free (Depositor)	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 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.