3HI0 | pdb_00003hi0

Crystal structure of Putative exopolyphosphatase (17739545) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	10.0000% MPD, 0.1M Acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.327	α = 90
b = 66.302	β = 90
c = 329.654	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-02-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97895,0.97835	SSRL	BL11-1

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	2.3	29.722	94.4	0.039	13.1	3.7		54859		-3	50.138

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	2.3	2.38	89.1		0.327	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.3	29.722	54848	2791	97.66	0.188	0.186	0.19	0.233	0.24	RANDOM	51.115

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]
-1.93			4.22		-2.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.825
r_dihedral_angle_4_deg	17.625
r_dihedral_angle_3_deg	14.251
r_scangle_it	6.688
r_dihedral_angle_1_deg	5.604
r_scbond_it	5.197
r_mcangle_it	2.621
r_mcbond_it	1.831
r_angle_refined_deg	1.387
r_angle_other_deg	0.98
r_mcbond_other	0.542
r_symmetry_vdw_other	0.262
r_nbd_refined	0.191
r_nbd_other	0.186
r_symmetry_vdw_refined	0.178
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.156
r_xyhbond_nbd_other	0.094
r_symmetry_hbond_refined	0.092
r_nbtor_other	0.084
r_chiral_restr	0.078
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7550
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing