5N0L | pdb_00005n0l

The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B18

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	20% polyethylene glycol 3350, 0.2 M sodium formate, 0.1 M Bis-tris-propane, pH 6.5 and protein solutions containing 10 mM isoleucine.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.89	α = 90
b = 190.39	β = 90
c = 43.51	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	PIXEL	DECTRIS PILATUS 6M-F		2015-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.68	56.19	100	0.067	0.999	17.1	8.1		115569

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.72	99.9		1.81	0.515		8.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2B18	1.68	56.19	109833	5726	99.96	0.15778	0.15406	0.16	0.2283	0.23	RANDOM	37.644

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]
0.79			-0.39		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.489
r_sphericity_free	35.621
r_sphericity_bonded	25.944
r_dihedral_angle_3_deg	15.788
r_dihedral_angle_4_deg	11.415
r_dihedral_angle_1_deg	9.683
r_scangle_other	8.695
r_long_range_B_refined	8.694
r_long_range_B_other	8.652
r_scbond_it	7.723
r_scbond_other	7.723
r_mcangle_it	7.591
r_mcangle_other	7.59
r_mcbond_other	6.31
r_mcbond_it	6.309
r_rigid_bond_restr	5.349
r_angle_refined_deg	2.538
r_angle_other_deg	1.319
r_chiral_restr	0.151
r_bond_refined_d	0.027
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7230
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing