4EIN

Crystal structure of mouse thymidylate synthase in binary complex with a substrate analogue and strong inhibitor, N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IHIPDB entry 3IHI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP278MES, PEG 8K, MgAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
3.4364.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.023α = 90
b = 87.956β = 96.44
c = 68.668γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.7520.0696.40.06510.12.290892
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7897.60.3522.1

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 DIFFRACTION3IHI structure was refined relative to collected diffraction dataTHROUGHOUTPDB entry 3IHI1.7520.0686322457095.190.208460.205940.25524RANDOM23.361
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.133
r_dihedral_angle_4_deg18.872
r_dihedral_angle_3_deg15.536
r_dihedral_angle_1_deg6.403
r_scangle_it4.379
r_scbond_it2.946
r_mcangle_it2.145
r_angle_refined_deg1.973
r_mcbond_it1.297
r_angle_other_deg1.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.133
r_dihedral_angle_4_deg18.872
r_dihedral_angle_3_deg15.536
r_dihedral_angle_1_deg6.403
r_scangle_it4.379
r_scbond_it2.946
r_mcangle_it2.145
r_angle_refined_deg1.973
r_mcbond_it1.297
r_angle_other_deg1.004
r_mcbond_other0.401
r_chiral_restr0.12
r_bond_refined_d0.024
r_gen_planes_refined0.011
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4600
Nucleic Acid Atoms
Solvent Atoms741
Heterogen Atoms48

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction