3BFI

E. Coli Thymidylate Synthase Y209M mutant complexed with 5-nitro-dUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TMS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52932.5 M AMMONIUM SULFATE, 20 MM REMARK 280 KH2PO4, 4 MM DTT, 4 MM 5-NO2-dUMP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2261.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.02α = 90
b = 133.02β = 90
c = 133.02γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293DIFFRACTOMETERENRAF-NONIUS FAST1997-11-13MSINGLE 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)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
12.235930.0810.0817.55.11997818431
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.4699

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3TMS2.226.091748994292.260.167580.16510.21799RANDOM30.051
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_deg36.111
r_dihedral_angle_4_deg22.342
r_dihedral_angle_3_deg17.347
r_dihedral_angle_1_deg6.421
r_scangle_it4.217
r_scbond_it2.656
r_mcangle_it1.711
r_angle_refined_deg1.657
r_mcbond_it0.973
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.111
r_dihedral_angle_4_deg22.342
r_dihedral_angle_3_deg17.347
r_dihedral_angle_1_deg6.421
r_scangle_it4.217
r_scbond_it2.656
r_mcangle_it1.711
r_angle_refined_deg1.657
r_mcbond_it0.973
r_nbtor_refined0.309
r_nbd_refined0.211
r_symmetry_vdw_refined0.163
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.133
r_chiral_restr0.108
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 Atoms2149
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MADNESSdata collection
PROCORdata reduction
PROCORdata scaling