2ENX

Structure of the family II inorganic pyrophosphatase from Streptococcus agalactiae at 2.8 resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I74	PDB ENTRY 1I74

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.2	298	0.4M ammonium phosphate monobasic, pH 4.2, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.96	α = 90
b = 181.96	β = 90
c = 132.61	γ = 120

Symmetry
Space Group	H 3 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	IMAGE PLATE	RIGAKU RAXIS IV		2005-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	19.5	99.6	0.14	0.14	12.3	4.2	20708	20700	-3	-3	40

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	96.2		0.3	0.3	6.2	4.4	1903

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 1I74	2.8	19.5	19668	1036	100	0.19565	0.1919	0.26695	RANDOM	18.164

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]
-1.2	-0.6		-1.2		1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.281
r_dihedral_angle_3_deg	19.307
r_dihedral_angle_4_deg	17.653
r_dihedral_angle_1_deg	6.247
r_angle_refined_deg	1.513
r_nbtor_refined	0.309
r_nbd_refined	0.237
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.094
r_symmetry_hbond_refined	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4714
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing