2GTA

Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR428.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	16% PEG 3350, 0.25 M Sodium Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.747	α = 90
b = 79.694	β = 90
c = 119.568	γ = 90

Symmetry
Space Group	P 21 21 21

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 4		2006-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97900	NSLS	X4A

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	2.9	30	99.5	0.095		12.1		24876			99.3

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)
	2.9	3.02	99.8		0.318		13.3	2813

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.9	29.89	1	23837	978	80.1	0.225	0.225	0.263	RANDOM	53.8

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]
-7.4			46.26		-38.86

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.5
c_angle_deg	1.3
c_improper_angle_d	0.73
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2938
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building