5N0L

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529120% 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 coefficientSolvent content
2.448.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.89α = 90
b = 190.39β = 90
c = 43.51γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6856.191000.0670.99917.18.1115569
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)RedundancyNumber Unique Reflections (All)
11.681.7299.91.810.5158.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2B181.6856.19109833572699.960.157780.154060.2283RANDOM37.644
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.489
r_sphericity_free35.621
r_sphericity_bonded25.944
r_dihedral_angle_3_deg15.788
r_dihedral_angle_4_deg11.415
r_dihedral_angle_1_deg9.683
r_scangle_other8.695
r_long_range_B_refined8.694
r_long_range_B_other8.652
r_scbond_it7.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.489
r_sphericity_free35.621
r_sphericity_bonded25.944
r_dihedral_angle_3_deg15.788
r_dihedral_angle_4_deg11.415
r_dihedral_angle_1_deg9.683
r_scangle_other8.695
r_long_range_B_refined8.694
r_long_range_B_other8.652
r_scbond_it7.723
r_scbond_other7.723
r_mcangle_it7.591
r_mcangle_other7.59
r_mcbond_other6.31
r_mcbond_it6.309
r_rigid_bond_restr5.349
r_angle_refined_deg2.538
r_angle_other_deg1.319
r_chiral_restr0.151
r_bond_refined_d0.027
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms7230
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing