5ULN

Synthesis of novel seleno ureido containing compounds as SLC-0111 analogs. Investigations on carbonic anhydrases activity, glutathione peroxidase and X-ray crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CQ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3281concentrated CA II at ~10 mg/mL was set up in SD-2 plates (Molecular Dimensions) with the following ratio of protein plus reservoir plus seeds: 250 nL + 225 nL + 25 nL. The plate was incubated at 8 C and the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3. Dry compound was added to the crystallization drop after crystals had formed and several days before data were c ollected.
Crystal Properties
Matthews coefficientSolvent content
2.1141.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.489α = 90
b = 41.563β = 104.48
c = 72.203γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102016-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX11.00800Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.3541.6940.0420.017131.37.350449
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3761.50.2840.1240.9486.36.11628

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 REPLACEMENTTHROUGHOUT4cq01.3541.648038239593.70.107380.105710.14261RANDOM13.843
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]
0.17-0.070.06-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.913
r_sphericity_free23.406
r_dihedral_angle_4_deg21.597
r_dihedral_angle_3_deg12.649
r_sphericity_bonded9.972
r_dihedral_angle_1_deg6.33
r_long_range_B_refined3.271
r_long_range_B_other3.27
r_scangle_other2.904
r_rigid_bond_restr2.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.913
r_sphericity_free23.406
r_dihedral_angle_4_deg21.597
r_dihedral_angle_3_deg12.649
r_sphericity_bonded9.972
r_dihedral_angle_1_deg6.33
r_long_range_B_refined3.271
r_long_range_B_other3.27
r_scangle_other2.904
r_rigid_bond_restr2.856
r_scbond_other2.602
r_scbond_it2.601
r_mcangle_other1.896
r_mcangle_it1.878
r_angle_refined_deg1.783
r_mcbond_it1.484
r_mcbond_other1.469
r_angle_other_deg1.034
r_chiral_restr0.124
r_bond_refined_d0.015
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 Atoms2064
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing