5IOT

Flavin-dependent thymidylate synthase R174A variant in complex with FAD and dUMP


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
2.0138.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.06α = 90
b = 115.86β = 90
c = 141.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-08-14MSINGLE 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)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
1289.5490.78.7654863

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 REPLACEMENTTHROUGHOUT4GT9289.5452046275390.210.18450.182770.21742RANDOM34.545
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]
-0.781.9-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.458
r_dihedral_angle_4_deg19.737
r_dihedral_angle_3_deg14.523
r_dihedral_angle_1_deg5.932
r_long_range_B_refined5.812
r_long_range_B_other5.777
r_scangle_other4.299
r_mcangle_it2.841
r_mcangle_other2.841
r_scbond_it2.706
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.458
r_dihedral_angle_4_deg19.737
r_dihedral_angle_3_deg14.523
r_dihedral_angle_1_deg5.932
r_long_range_B_refined5.812
r_long_range_B_other5.777
r_scangle_other4.299
r_mcangle_it2.841
r_mcangle_other2.841
r_scbond_it2.706
r_scbond_other2.706
r_mcbond_it1.955
r_mcbond_other1.955
r_angle_refined_deg1.489
r_angle_other_deg1.198
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms7168
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms292

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing