3JSN

Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72871.6M DL-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.3748.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.877α = 90
b = 79.798β = 90
c = 101.675γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173CCDADSC QUANTUM 2102009-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-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
11.93092.60.08116.54.125917
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)
1.91.9774.70.3383.92047

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.93024543133392.270.195370.193080.23498RANDOM31.993
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]
-1.322.46-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.808
r_dihedral_angle_3_deg17.8
r_dihedral_angle_4_deg17.216
r_scangle_it6.631
r_dihedral_angle_1_deg6.619
r_scbond_it3.931
r_mcangle_it2.393
r_angle_refined_deg1.931
r_mcbond_it1.257
r_chiral_restr0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.808
r_dihedral_angle_3_deg17.8
r_dihedral_angle_4_deg17.216
r_scangle_it6.631
r_dihedral_angle_1_deg6.619
r_scbond_it3.931
r_mcangle_it2.393
r_angle_refined_deg1.931
r_mcbond_it1.257
r_chiral_restr0.141
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2415
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling