3KS5

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	0.2000M Ca(OAc)2, 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.153	α = 90
b = 84.153	β = 90
c = 214.882	γ = 90

Symmetry
Space Group	P 41 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-04-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97855,0.97783	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	2.05	30.069	99.4	0.08	11.54	7		49371		-3	34.435

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)
	2.05	2.12	95.9		0.971	1.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.05	30.069	49285	2492	99.69	0.214	0.212	0.244	RANDOM	46.781

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]
0.05			0.05		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.211
r_dihedral_angle_4_deg	17.496
r_dihedral_angle_3_deg	11.941
r_scangle_it	5.753
r_dihedral_angle_1_deg	4.78
r_scbond_it	4.579
r_mcangle_it	2.791
r_mcbond_it	2.073
r_angle_refined_deg	1.515
r_angle_other_deg	1.184
r_mcbond_other	1.022
r_nbd_refined	0.187
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.166
r_nbd_other	0.162
r_symmetry_hbond_refined	0.157
r_symmetry_vdw_other	0.146
r_symmetry_vdw_refined	0.143
r_nbtor_other	0.084
r_chiral_restr	0.072
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3824
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	70

Software

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