3NU0

Design, Synthesis, Biological Evaluation and X-ray Crystal Structure 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
1VAPOR DIFFUSION, HANGING DROP6.9293100 mM KPO4, 69% saturated AmSO4, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 200K, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.395α = 90
b = 84.395β = 90
c = 78.193γ = 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 BL9-20.975SSRLBL9-2

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
11.3533.11000.0630.0662712.5569239455872227
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)
11.351.421000.390.458.612.16657

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTu0721.3533.1243285230299.990.2120.181490.180040.20927RANDOM15.638
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.322
r_dihedral_angle_4_deg16.837
r_dihedral_angle_3_deg16.116
r_dihedral_angle_1_deg6.858
r_scangle_it4.993
r_scbond_it3.598
r_angle_refined_deg2.992
r_mcangle_it2.343
r_mcbond_it1.416
r_chiral_restr0.511
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.322
r_dihedral_angle_4_deg16.837
r_dihedral_angle_3_deg16.116
r_dihedral_angle_1_deg6.858
r_scangle_it4.993
r_scbond_it3.598
r_angle_refined_deg2.992
r_mcangle_it2.343
r_mcbond_it1.416
r_chiral_restr0.511
r_bond_refined_d0.035
r_gen_planes_refined0.02
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms99

Software

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