Purpose The relative biological effectiveness (RBE) in the presence or absence of CHK2 was estimated at the Korean National Cancer Center Proton Therapy Center (NCCPTC). Methods and Materials The proton beam was fixed at 210 MeV with 6-cm spread-out Bragg peaks (SOBPs) because this is expected to be the most frequently used clinical setting. X-rays were obtained using a 6-MV conventional linear accelerator. The RBE was estimated from the survival of jejunal crypt in C3H/He and Chk2 -/- mice. Results The estimated RBEs of the NCCPTC at the middle of the SOBP were 1.10 and 1.05 in the presence and absence of CHK2, respectively. The doses that reduced the number of regenerated crypt per jejunal circumference to 20 (D 20) in C3H/He mice were 14.8 Gy (95% confidence interval [CI], 13.7–15.9) for X-rays and 13.5 Gy (95% CI, 14.5–15.5) for protons. By contrast, the doses of D 20 in Chk2 -/- mice were 15.7 Gy (95% CI, 15.0–16.4) and 14.9 Gy (95% CI, 14.0–15.8) for X-rays and protons, respectively. Conclusions The RBE of the NCCPTC is clearly within the range of RBEs determined at other facilities and is consistent with the generic RBE value of 1.10 for 150- to 250-MeV beams. The mutation of Chk2 gave rise to radioresistance but exhibited similar RBE.