3NTZ

Design, Synthesis, Biological Evaluation and X-ray Crystal Structures of Novel Classical 6,5,6-tricyclicbenzo[4,5]thieno[2,3-d]pyrimidines as Dual Thymidylate Synthase and Dihydrofolate Reductase Inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U72U072

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.9293100 mM KPO4, 66% saturated AmSO4, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 200K, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4950.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.287α = 90
b = 84.287β = 90
c = 77.792γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 325 mm CCDMIRRORS2008-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.3553.221000.0530.0315.33.7452602
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.421000.610.361.63.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTU0721.3526.61497294297622821000.1870.1860.203RANDOM18.91
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.899
r_dihedral_angle_4_deg17.985
r_dihedral_angle_3_deg14.292
r_dihedral_angle_1_deg6.783
r_scangle_it5.568
r_scbond_it3.754
r_angle_refined_deg2.844
r_mcangle_it2.441
r_mcbond_it1.498
r_chiral_restr0.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.899
r_dihedral_angle_4_deg17.985
r_dihedral_angle_3_deg14.292
r_dihedral_angle_1_deg6.783
r_scangle_it5.568
r_scbond_it3.754
r_angle_refined_deg2.844
r_mcangle_it2.441
r_mcbond_it1.498
r_chiral_restr0.525
r_bond_refined_d0.031
r_gen_planes_refined0.018
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 Atoms1502
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms108

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling