3KZP | pdb_00003kzp

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Listaria monocytigenes

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	293	0.2 M Ca acetate, 0.1 M Na cacodilate, 9% PEG 8K, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.766	α = 90
b = 92.04	β = 90
c = 96.21	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	ADSC QUANTUM 315	MIRROR	2008-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9786	APS	19-ID

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	50	93.7	0.091	0.091	21.885	6.5	34443	34443		-3

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	2.03	88		0.513	0.513	2.8	5.9	1520

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	50	34327	34327	1714	93.86	0.187	0.187	0.185	0.2	0.239	0.25	RANDOM	13.14

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]
0.11			1.44		-1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.118
r_dihedral_angle_4_deg	15.007
r_dihedral_angle_3_deg	13.975
r_dihedral_angle_1_deg	6.303
r_scangle_it	4.135
r_scbond_it	2.698
r_angle_refined_deg	1.75
r_mcangle_it	1.617
r_angle_other_deg	0.999
r_mcbond_it	0.959
r_mcbond_other	0.296
r_chiral_restr	0.104
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3771
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	18

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing