2R6O

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	0.2M MgCl2, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.051	α = 90
b = 63.141	β = 90
c = 173.282	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	CUSTOM-MADE		2007-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97857	APS	19-BM

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	1.8	50	97.3	0.06	39.67	10.6	51848	50452		-3	27.4

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	1.8	1.86	90.1		0.454	3.26	8.5	4585

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	27.7	47788	47788	2554	97.22	0.1898	0.1898	0.18829	0.21756	RANDOM	30.8

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]
2.24			-0.57		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.259
r_dihedral_angle_4_deg	17.369
r_dihedral_angle_3_deg	14.532
r_dihedral_angle_1_deg	5.152
r_scangle_it	3.054
r_scbond_it	2.014
r_angle_refined_deg	1.212
r_mcangle_it	1.145
r_mcbond_it	0.739
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.282
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.139
r_metal_ion_refined	0.127
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3835
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing