3B9H

E. coli thymidylate synthase complexed with 5-NITRO-2'-DEOXY URIDINE


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52932.1 M ammonium sulfate, 20 mM KH2PO4, 4 mM DTT, 4 mM 5-nitro-dump, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7955.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.6α = 90
b = 71.6β = 90
c = 115.32γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293DIFFRACTOMETERENRAF-NONIUS FASTgraphite crystal monochrometer1997-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5711.5418

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
12.4930930.1410.25.31243311592

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1TSN2.4930115921159269993.240.172240.16820.23262RANDOM26.359
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]
0.150.070.15-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.205
r_dihedral_angle_4_deg20.548
r_dihedral_angle_3_deg18.4
r_dihedral_angle_1_deg6.835
r_scangle_it3.981
r_scbond_it2.431
r_angle_refined_deg1.71
r_mcangle_it1.569
r_mcbond_it0.864
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.205
r_dihedral_angle_4_deg20.548
r_dihedral_angle_3_deg18.4
r_dihedral_angle_1_deg6.835
r_scangle_it3.981
r_scbond_it2.431
r_angle_refined_deg1.71
r_mcangle_it1.569
r_mcbond_it0.864
r_nbtor_refined0.316
r_nbd_refined0.232
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.129
r_chiral_restr0.113
r_symmetry_hbond_refined0.093
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2153
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MADNESSdata collection
PROCORdata reduction
PROCORdata scaling