5IOR

Flavin-dependent thymidylate synthase in complex with FAD and 2'-deoxyuridine-5'-monosulfate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.6293.157% PEG 4K, 100 mM NaCl, 100 mM Na/K phosphate, pH 6.6
Crystal Properties
Matthews coefficientSolvent content
3.2862.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.679α = 90
b = 109.679β = 90
c = 119.864γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03320APS23-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
11.9580.9299.720.414.627043

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 REPLACEMENTTHROUGHOUT4GT91.9580.9225671127099.990.163410.162040.19148RANDOM32.196
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]
-0.99-0.991.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.313
r_dihedral_angle_4_deg18.241
r_dihedral_angle_3_deg13.055
r_dihedral_angle_1_deg6.017
r_long_range_B_refined5.041
r_long_range_B_other4.986
r_scangle_other2.844
r_scbond_it1.747
r_mcangle_it1.742
r_mcangle_other1.741
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.313
r_dihedral_angle_4_deg18.241
r_dihedral_angle_3_deg13.055
r_dihedral_angle_1_deg6.017
r_long_range_B_refined5.041
r_long_range_B_other4.986
r_scangle_other2.844
r_scbond_it1.747
r_mcangle_it1.742
r_mcangle_other1.741
r_scbond_other1.734
r_angle_refined_deg1.342
r_mcbond_it1.12
r_mcbond_other1.12
r_angle_other_deg0.786
r_chiral_restr0.082
r_bond_refined_d0.009
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 Atoms1801
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing