4CC5

Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JSLPDB ENTRY 3JSL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.51.6M (NH4)2SO4, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2344.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.363α = 90
b = 39.523β = 90.13
c = 48.587γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.888597.40.1272.9268552
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)
11.881.993.40.462.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3JSL1.8885.1824676139096.950.19320.189320.264RANDOM25.023
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]
-1.790.652.18-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.34
r_dihedral_angle_4_deg18.602
r_dihedral_angle_3_deg14.015
r_long_range_B_refined6.068
r_dihedral_angle_1_deg5.874
r_scbond_it2.722
r_scbond_other2.711
r_mcbond_it1.625
r_mcbond_other1.616
r_angle_refined_deg1.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.34
r_dihedral_angle_4_deg18.602
r_dihedral_angle_3_deg14.015
r_long_range_B_refined6.068
r_dihedral_angle_1_deg5.874
r_scbond_it2.722
r_scbond_other2.711
r_mcbond_it1.625
r_mcbond_other1.616
r_angle_refined_deg1.473
r_angle_other_deg0.774
r_chiral_restr0.085
r_bond_refined_d0.011
r_bond_other_d0.001
r_gen_planes_refined
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_mcangle_it
r_mcangle_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2488
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling