1W25

Response regulator PleD in complex with c-diGMP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.2		CRYSTALS WERE OBTAINED AT ROOM TEMPERATURE BY HANGING DROP VAPOUR DIFFUSION. FOR THIS, PLED AT A NOMINAL CONCENTRATION OF 10 MG/ML IN 20 MM TRIS-HCL (PH 8.0), 100 MM NACL, 1 MM DTT, 2 MM MGCL2 AND 0.8 MM C-DIGMP6 WAS MIXED WITH THE RESERVOIR (1.0 M GLYCINE PH 9.2, 2 % DIOXANE, 14.5 % POLYETHYLENE GLYCOL 20K) AT A RATIO 1 TO 1.

Crystal Properties
Matthews coefficient	Solvent content
3.9	69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.87	α = 90
b = 135.87	β = 90
c = 169.247	γ = 90

Symmetry
Space Group	P 42 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		2003-12-14	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	2.7	60.86	99.3	0.08	16.42	5.7		43706		-3.7

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	2.7	2.72	98.7		0.36	2.96	5.48

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	2.7	50	41469	2202	98.9	0.212	0.21	0.239	RANDOM	25.61

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]
-0.07			-0.07		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.956
r_dihedral_angle_4_deg	16.945
r_dihedral_angle_3_deg	16.4
r_dihedral_angle_1_deg	5.586
r_scangle_it	3.706
r_scbond_it	2.416
r_mcangle_it	1.307
r_angle_refined_deg	1.211
r_mcbond_it	1.129
r_angle_other_deg	0.773
r_symmetry_vdw_other	0.295
r_nbd_refined	0.201
r_mcbond_other	0.18
r_symmetry_vdw_refined	0.177
r_nbd_other	0.17
r_xyhbond_nbd_refined	0.108
r_nbtor_other	0.083
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	6962
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	233

Software

Software
Software Name	Purpose
DM	model building
TRUNCATE	data scaling
SHELXD	phasing
SHARP	phasing
SOLOMON	phasing
DM	phasing
REFMAC	refinement