2WB4

activated diguanylate cyclase PleD in complex with c-di-GMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V0N	PDB ENTRY 2V0N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		PROTEIN SOLUTION\: 100 MICROM PLED, 0.2 MM C-DI-GMP, 2 MM GMPCPP, 1 MM BECL2, 10 MM NAF, 10 MM MGCL2 RESERVOIR\: 0.1 M HEPES, PH 8.0, 0.73 M NA2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.46	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.56	α = 90
b = 127.43	β = 90
c = 88.13	γ = 90

Symmetry
Space Group	P 21 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	MARRESEARCH		2006-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	2.4	72.48	87	0.1	5.6	3.45		42374		1.8

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	2.5	2.64	62.4		0.28	2.23	3.26

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 2V0N	2.8	60	31368	1691	94.49	0.24053	0.23906	0.26816	RANDOM	11.413

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]
-0.69			-1.28		1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.452
r_dihedral_angle_4_deg	20.943
r_dihedral_angle_3_deg	16.815
r_dihedral_angle_1_deg	5.625
r_scangle_it	5.094
r_scbond_it	3.148
r_mcangle_it	1.772
r_angle_refined_deg	1.599
r_angle_other_deg	1.429
r_mcbond_it	0.955
r_chiral_restr	0.076
r_bond_refined_d	0.016
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6908
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	256

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing