Table 1.
Diffraction and Refinement Statistics
| KRM1ECD | KRM1ECD | KRM1ECD | KRM1ECD | LRP6PE3PE4-DKKCRD2-KRM1ECD | |
|---|---|---|---|---|---|
| Crystal form | I | I | II | III | I |
| X-ray source | Diamond i04 | Diamond i03 | Diamond i03 | Diamond i04 | Diamond i04 |
| Wavelength (Å) | 0.9793 | 0.9700 | 0.9700 | 0.9795 | 0.9795 |
| Space group | P3121 | P3121 | P43 | P41212 | C2221 |
| Unit cell a/α (Å/°) | 50.9/90 | 50.5/90 | 65.8/90 | 67.8/90 | 86.9/90 |
| b/β (Å/°) | 50.9/90 | 50.5/90 | 65.8/90 | 67.8/90 | 100.1/90 |
| c/γ (Å/°) | 188.4/120 | 187.4/120 | 75.0/90 | 198.2/90 | 270.7/90 |
| Wilson B factor (Å2) | 31 | 41 | 76 | 77 | NA |
| Resolution range (Å) | 47.10–1.90 (1.95–1.90) | 62.47–2.10 (2.16–2.10) | 75.00–2.80 (2.99–2.80) | 67.80–3.20 (3.42–3.20) | 67.68–3.50 (7.16–6.40, 3.92–3.50) |
| Unique reflections | 23,300 (1,524) | 17,089 (1,428) | 7,964 (1,448) | 8,171 (1,343) | 8,070 (723, 645) |
| Average multiplicity | 9.1 (9.2) | 5.2 (5.3) | 3.7 (3.7) | 22.7 (12.6) | 3.8 (3.5, 4.4) |
| Completeness (%) | 99.8 (98.5) | 100 (100) | 99.8 (100) | 98.8 (93.4) | 51.6 (98.5, 14.1) |
| <I/σI> | 11.4 (1.7) | 12.0 (1.7) | 14.9 (1.5) | 13.1 (1.9) | 4.6 (4.1, 2.2) |
| Rmerge (%) | 14.8 (158.3) | 9.3 (98.0) | 6.2 (98.9) | 29.8 (142.2) | 44.9 (40.5, 114.2) |
| Rpim (%) | 15.7 (55.3) | 10.3 (109.0) | 3.7 (53.8) | 6.3 (40.0) | 24.7 (23.9, 59.9) |
| Refinement | |||||
| Rwork (%) | 17.9 | 18.4 | 21.6 | 20.2 | 32.1 |
| Rfree (%) | 22.7 | 23.2 | 30.7 | 27.1 | 35.5 |
| No. of Non-Hydrogen Atoms | |||||
| Protein | 2,260 | 2,301 | 2,102 | 2,305 | 7,730 |
| N-glycans | 42 | 42 | 28 | 28 | 0 |
| Water | 79 | 54 | 0 | 2 | 0 |
| Ligands | 6 | 6 | 2 | 5 | 0 |
| Average B factor (Å2) | |||||
| Protein | 63 | 65 | 108 | 84 | – |
| N-glycans | 35 | 46 | 102 | 18 | – |
| Water | 68 | 85 | – | 75 | – |
| Ligands | 36 | 47 | 91 | 75 | 66 |
| RMSD from Ideality | |||||
| Bond lengths (Å) | 0.020 | 0.016 | 0.019 | 0.016 | 0.004 |
| Bond angles (°) | 2.050 | 1.748 | 1.952 | 1.796 | 0.770 |
| Ramachandran Plot | |||||
| Favored (%) | 96.8 | 95.5 | 96.9 | 94.9 | 92.3 |
| Allowed (%) | 99.7 | 100.0 | 100.0 | 99.7 | 99.8 |
| Number of outliers | 1 | 0 | 0 | 1 | 2 |
| PDB code | 5FWS | 5FWT | 5FWU | 5FWV | 5FWW |
Values in parentheses refer to the highest-resolution shell. An additional shell given for the ternary complex corresponds to the last shell with near-complete diffraction data. NA, not announced.