3BHL

E.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahydrofolate at 1.4 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TSCpdb entry 2TSC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52932.5 M ammonium sulfate, 20 mm KH2PO4, 4mm DTT, 4 mM 5-NO2dump, 4MM methylenetetrahydrofolate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.87α = 90
b = 124.87β = 90
c = 66.394γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.9APS14-BM-D

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
11.4105.411000.07618.66.4115632115632
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.451000.453.26.3

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 SYNTHESISTHROUGHOUTpdb entry 2TSC1.425109776579999.740.175640.17420.20299RANDOM10.792
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.845
r_dihedral_angle_4_deg23.521
r_dihedral_angle_3_deg13.556
r_dihedral_angle_1_deg6.453
r_scangle_it3.394
r_scbond_it2.271
r_angle_other_deg1.984
r_angle_refined_deg1.786
r_mcangle_it1.511
r_mcbond_it0.854
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.845
r_dihedral_angle_4_deg23.521
r_dihedral_angle_3_deg13.556
r_dihedral_angle_1_deg6.453
r_scangle_it3.394
r_scbond_it2.271
r_angle_other_deg1.984
r_angle_refined_deg1.786
r_mcangle_it1.511
r_mcbond_it0.854
r_chiral_restr0.302
r_symmetry_vdw_other0.302
r_mcbond_other0.249
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.132
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4306
Nucleic Acid Atoms
Solvent Atoms437
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling