2Y1O | pdb_00002y1o

Dual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis and Binding Mode Studies


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UAGPDB ENTRY 1UAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.46.0 MG/ML MURD, 20 MM HEPES, PH 7.4, 200 MM NACL, 5 MM DITHIOTHREITOL, 0.05% (W/V) NAN3 0.1. M HEPES PH 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL
Crystal Properties
Matthews coefficientSolvent content
3.0759.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.844α = 90
b = 65.844β = 90
c = 135.747γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.4946.5682.80.0427.74.591441325.693
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.5852.20.4733.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1UAG1.4946.567941988261000.207490.205120.210.228450.23RANDOM23.543
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]
0.240.24-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.752
r_dihedral_angle_4_deg18.828
r_dihedral_angle_3_deg12.842
r_dihedral_angle_1_deg6.544
r_scangle_it6.065
r_scbond_it3.829
r_mcangle_it2.505
r_mcbond_it1.631
r_angle_refined_deg1.612
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.752
r_dihedral_angle_4_deg18.828
r_dihedral_angle_3_deg12.842
r_dihedral_angle_1_deg6.544
r_scangle_it6.065
r_scbond_it3.829
r_mcangle_it2.505
r_mcbond_it1.631
r_angle_refined_deg1.612
r_chiral_restr0.128
r_bond_refined_d0.013
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
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 Atoms3278
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing