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. Author manuscript; available in PMC: 2013 Jun 1.
Published in final edited form as: Proteins. 2012 Mar 13;80(6):1545–1559. doi: 10.1002/prot.24041

Table I.

Summary of crystal parameters, data collection, and refinement statistics

TM0077-SeMet TM0077-Native TM0077-PMS TM0077-DEP
Space group P 21 P 21 21 21 P 21 21 21 P 21 21 21
Unit cell parameters a=152.64Å b=130.95Å
c=157.82Å β=118.90°		 a=103.46Å
b=103.79Å
c=221.02Å		 a=103.57Å
b=104.50Å
c=221.61Å		 a=103.80Å
b=104.43Å
c=221.64Å
Data collection λ1 MAD-Se λ2 MAD-Se
 Wavelength (Å) 0.9791 0.9183 0.9765 0.9765 0.9765
 Resolution range (Å) 29.6 – 2.10 29.6 – 2.10 48.8 – 2.50 49.0 – 2.40 49.0 – 2.12
 No. observations 1,119,236 1,100,249 1,222,016 765,546 989,949
 No. unique reflections 293,140 291,757 83,045 94,681 123,070
 Completeness (%) 93.0 (61.8)a 92.6 (60.8) 100 (100) 100 (100) 89.8 (53.5)
 Mean I/σ(I) 9.1 (2.4)a 9.6 (2.2) 14.4 (2.9) 11.5 (3.4) 15.3 (2.2)
 Rmerge on I (%) 12.3 (52.5) a 11.9 (57.9) 20.7 (109.7) c 18.0 (67.4) 9.5 (51.9)
 Rmeas on I (%) 14.3 (62.2) a 13.9 (68.7) 21.4 (113.6) 19.2 (71.9) 10.2 (60.2)
 Rpim on I (%) 7.2 (32.7) a 7.1 (36.2) 5.5 (29.2) 6.7 (24.9) 3.5 (29.2)
 Highest resolution shell (Å) 2.15 – 2.10 2.15 – 2.10 2.56 – 2.50 2.46 – 2.40 2.18 – 2.12
Model and refinement statistics
 Resolution range (Å) 29.6 – 2.10 48.8 – 2.50 49.0–2.40 49.0 – 2.12
 No. reflections (total) 293,097 b 83,045 94,680 122,994
 No. reflections (test) 14,726 4,200 4,742 6,188
 Completeness (% total) 92.8 100.0 100.0 89.8
 Data set used in refinement λ1 MAD-Se
 Cutoff criteria |F| > 0 |F| > 0 |F| > 0 |F| > 0
 Rcryst 0.186 0.167 0.160 0.167
 Rfree 0.223 0.212 0.208 0.205
Stereochemical parameters
Restraints (RMSD observed)
 Bond angle (°) 1.48 1.47 1.53 1.44
 Bond length (Å) 0.018 0.017 0.017 0.015
Av. isotropic B-value (Å2) 27.9 24.7 19.4 19.6
ESU based on Rfree 0.17 0.25 0.22 0.18
Water molecules/other solvent molecules 2,464/1 507/24 946/17 987/23
PDB ID 1vlq 3m81 3m82 3m83
a

Highest resolution shell

ESU = Estimated overall coordinate error 16,66.

Rmerge=ΣhklΣi|Ii(hkl)-<I(hkl)>|/ΣhklΣiIi(hkl), Rmeas(redundancy-independent Rmerge)=Σhkl[Nhkl/(Nhkl-1)]1/2Σi|Ii(hkl)-<I(hkl)>|/ΣhklΣiIi(hkl), and Rpim(precision-indicating Rmerge)=Σhkl[1/(Nhkl-1)]1/2Σi|Ii(hkl)-<I(hkl)>|/ΣhklΣiIi(hkl) 67–69.

Rcryst = Σ| |Fobs|-|Fcalc| |/Σ|Fobs| where Fcalc and Fobs are the calculated and observed structure factor amplitudes, respectively.

Rfree = as for Rcryst, but for 5.0 % of the total reflections chosen at random and omitted from refinement.

b

Typically, the number of unique reflections used in refinement is slightly less than the total number that were integrated and scaled. Reflections are excluded due to systematic absences, negative intensities, and rounding errors in the resolution limits and cell parameters.

c

Rmerge of the highest resolution shell is high due to high redundancy (14.7). However, the completeness and mean I/σ of the highest resolution shell are reasonable, and these data were included in the refinement.