2W27

CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN, IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CALCIUM

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.2M SODIUM ACETATE THRIHYDRATE, 0.1M IMIDAZOLE, 0.1M TRIS HYDROCHLORIDE, 28% PEG 4000, 3% GLYCEROL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.167	α = 90
b = 124.521	β = 90
c = 168.751	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	MARRESEARCH		2007-02-03	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	2.8	69.84	87.2	0.1	5.6	3.41		21459

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	2.8	2.95	73		0.42	1.66	2.83

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 2BAS	2.8	30	20362	1046	86.3	0.228	0.226	0.275	RANDOM	32.96

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]
7.38			-8.51		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.395
r_dihedral_angle_3_deg	18.174
r_dihedral_angle_4_deg	15.567
r_dihedral_angle_1_deg	5.846
r_scangle_it	3.431
r_scbond_it	2.281
r_mcangle_it	1.401
r_angle_refined_deg	1.198
r_mcbond_it	0.905
r_angle_other_deg	0.833
r_symmetry_vdw_other	0.306
r_metal_ion_refined	0.303
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.222
r_nbtor_refined	0.192
r_nbd_other	0.19
r_mcbond_other	0.148
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.102
r_nbtor_other	0.086
r_chiral_restr	0.066
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
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	6634
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing