3G5J

Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52920.2 M Lithium citrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.5165

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.489α = 90
b = 60.192β = 108.62
c = 79.107γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM Q315rMIRRORS2009-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.764094.50.07818.52.9405142
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.7959.30.4152.22.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.764024049438452204294.80.1740.1720.198RANDOM13.72
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]
-1.08-1.963.47-3.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.455
r_dihedral_angle_4_deg20.907
r_dihedral_angle_3_deg14.407
r_dihedral_angle_1_deg5.28
r_scangle_it4.704
r_scbond_it2.874
r_mcangle_it1.638
r_angle_refined_deg1.553
r_angle_other_deg0.934
r_mcbond_it0.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.455
r_dihedral_angle_4_deg20.907
r_dihedral_angle_3_deg14.407
r_dihedral_angle_1_deg5.28
r_scangle_it4.704
r_scbond_it2.874
r_mcangle_it1.638
r_angle_refined_deg1.553
r_angle_other_deg0.934
r_mcbond_it0.914
r_mcbond_other0.307
r_chiral_restr0.099
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2085
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms26

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
SHELXCDphasing
SHELXEmodel building
CCP4model building
Cootmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
ARPmodel building