6QXG

Crystal structure of His-tag human thymidylate synthase (HT-hTS) in complex with FdUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HWY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929327-30 % wt/vol PEG4000, 30 mM ammonium sulfate and 0.1 M TRIS, pH 9
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.22α = 90
b = 61.98β = 98.96
c = 169.363γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.0833.3799.40.0910.1030.0480.9957.54.563324237.05
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.1998.80.5440.6170.2870.85124.5

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 REPLACEMENTTHROUGHOUT1HWY2.0832.3659309318197.860.183260.1810.2248RANDOM82.927
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]
-0.14-0.060.19-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.439
r_dihedral_angle_4_deg19.412
r_dihedral_angle_3_deg17.199
r_long_range_B_refined14.935
r_dihedral_angle_1_deg7.282
r_mcangle_it4.214
r_scbond_it3.086
r_mcbond_it2.609
r_angle_refined_deg2.01
r_chiral_restr0.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.439
r_dihedral_angle_4_deg19.412
r_dihedral_angle_3_deg17.199
r_long_range_B_refined14.935
r_dihedral_angle_1_deg7.282
r_mcangle_it4.214
r_scbond_it3.086
r_mcbond_it2.609
r_angle_refined_deg2.01
r_chiral_restr0.137
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6786
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing