Crystal Structure of Mouse Thymidylate Synthase in Tertiary Complex with dUMP and Raltitrexed Reveals N-Terminus Architecture and Two Different Active Site Conformations

Table 1

Data collection and refinement statistics/PDB code 4EB4. Values in parentheses are for the highest resolution shell.

Data collection
Space group	P212121
Cell dimensions	𝑎=101.80 Å, 𝑏=114.22 Å, 𝑐=123.65 Å; 𝛼=𝛽=𝛾=90^∘
Beamline	Bessy 14.1
Wavelength [Å]	0.918
Resolution [Å]	20.04–1.74 (1.76–1.74)
𝑅merge^∗	0.054 (0.556)
Unique reflections	148229
Completeness [%]	99.9 (100)
Redundancy	3.6 (3.5)
⟨𝐼/𝜎(𝐼)⟩	21
Refinement
Resolution [Å]	1.74 (1.78–1.74)
Number of reflections	148148 (9725)
𝑅^∗∗	0.19 (0.31)
𝑅free^∗∗∗	0.24 (37)
Average B factor [Å^2]:
Overall	31
Polypeptide chain A	24
Polypeptide chain B	24
Polypeptide chain C	35
Polypeptide chain D	36
RMS deviations from ideal values for refined atoms
Bond lengths [Å]	0.022
Bond angles [°]	1.967
Ramachandran’s plot assignments
The most favored	936 (92.0%)
Additionally allowed	77 (7.6%)
Generously allowed	4 (0.4%)
Disallowed	0 (0.0%)

^∗𝑅_merge=∑_hkl∑_𝑖|𝐼_𝑖(hkl)−⟨𝐼(hkl)⟩|/∑_hkl∑_𝑖𝐼_𝑖(hkl), where 𝐼_𝑖(hkl) is the integrated intensity of a given reflection and ⟨𝐼(hkl)⟩ is the mean intensity of multiple corresponding symmetry-related reflections.
^∗∗𝑅=∑_hkl||𝐹_obs|−|𝐹_calc||/∑_hkl|𝐹_obs|, where 𝐹_obs and 𝐹_calc are the observed and calculated structure factors, respectively.
^∗∗∗𝑅_free is 𝑅 calculated using a randomly chosen 1000 reflections that were excluded from the refinement.