5IOS

Flavin-dependent thymidylate synthase R90A variant in complex with FAD and deoxyuridine monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GT9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8293.1540-50% PEG 200, 0-150 mM NaCl, 100 mM Tris-HCl pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.0239.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.071α = 90
b = 116.217β = 90
c = 141.007γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.989.6899.50.07322.96.670476

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4GT91.989.6866829355799.260.179620.177980.21062RANDOM36.745
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]
1.68-0.23-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.671
r_dihedral_angle_4_deg16.052
r_dihedral_angle_3_deg13.902
r_long_range_B_refined6.418
r_long_range_B_other6.405
r_dihedral_angle_1_deg5.949
r_scangle_other4.901
r_mcangle_it3.146
r_mcangle_other3.146
r_scbond_it3.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.671
r_dihedral_angle_4_deg16.052
r_dihedral_angle_3_deg13.902
r_long_range_B_refined6.418
r_long_range_B_other6.405
r_dihedral_angle_1_deg5.949
r_scangle_other4.901
r_mcangle_it3.146
r_mcangle_other3.146
r_scbond_it3.017
r_scbond_other3.016
r_mcbond_it2.208
r_mcbond_other2.208
r_angle_refined_deg1.483
r_angle_other_deg0.833
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7166
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms292

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing