2EB0

Crystal structure of Methanococcus jannaschii putative family II inorganic pyrophosphatase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HAW	PDB ENTRY 2HAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	25% PEG3350, 0.2M NaCl, 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.843	α = 90
b = 146.761	β = 90
c = 54.286	γ = 90

Symmetry
Space Group	P 21 21 2

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	RIGAKU JUPITER 210		2006-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1	SPring-8	BL26B2

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	2.2	50	99.3	0.113	18	8.7		30549			17.2

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	2.2	2.28	94.3		0.361	3.31	4.9	2856

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2HAW	2.2	37.44	28989	2903	95.5	0.205	0.205	0.271	RANDOM	34.7

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]
-10.18			2.33		7.85

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.8
c_scangle_it	11.16
c_mcangle_it	7.58
c_scbond_it	7.4
c_mcbond_it	4.76
c_angle_deg	1.2
c_improper_angle_d	0.75
c_bond_d	0.006
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4774
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing