5IOQ

Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine


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
2.0339.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.19α = 90
b = 116.113β = 90
c = 141.891γ = 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
11.9389.8698.10.09422.87.667137

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 REPLACEMENTTHROUGHOUT4GT91.9389.8662459331896.170.17230.170720.2018RANDOM39.126
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]
1.3-1-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.945
r_dihedral_angle_4_deg15.9
r_dihedral_angle_3_deg13.656
r_long_range_B_refined7.288
r_long_range_B_other7.288
r_dihedral_angle_1_deg5.832
r_scangle_other5.626
r_mcangle_it3.821
r_mcangle_other3.821
r_scbond_it3.487
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.945
r_dihedral_angle_4_deg15.9
r_dihedral_angle_3_deg13.656
r_long_range_B_refined7.288
r_long_range_B_other7.288
r_dihedral_angle_1_deg5.832
r_scangle_other5.626
r_mcangle_it3.821
r_mcangle_other3.821
r_scbond_it3.487
r_scbond_other3.487
r_mcbond_it2.656
r_mcbond_other2.655
r_angle_refined_deg1.475
r_angle_other_deg1.121
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.005
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 Atoms7142
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms367

Software

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