Table 1.
Data collection and refinement statistics of human WDR5.
| Dataseta | Human WDR5 | ||||
|---|---|---|---|---|---|
| WDR5-apo | WDR5-Rme0 | WDR5-Rme1 | WDR5-Rme2s | WDR5-H3R2me1 | |
| Unit cell data | |||||
| Space group | P21212 | P21212 | P21212 | P21212 | C2221 |
| Cell parameters (Å, °) | a = 81.57, b = 86.10, c = 39.96 α, β, γ = 90 |
a = 81.19, b = 86.70, c = 40.96 α, β, γ = 90 |
a = 81.07, b = 86.22, c = 40.76 α, β, γ = 90 |
a = 81.05, b = 86.29, c = 40.87 α, β, γ = 90 |
a = 78.29, b = 98.63, c = 80.26 α, β, γ = 90 |
| Vm (Å3/Dalton) | 2.1 | 2.1 | 2.1 | 2.1 | 2.3 |
| Number of subunits in the asymmetric unit | 1 | 1 | 1 | 1 | 1 |
| Data collection | |||||
| Beamline | LRL-CAT | LRL-CAT | LRL-CAT | LRL-CAT | LRL-CAT |
| Wavelength (Å) | 0.97931 | 0.97931 | 0.97931 | 0.97931 | 0.97931 |
| Temperature (K) | 100 | 100 | 100 | 100 | 100 |
| Resolution range (Å) | 59.22 – 1.85 (1.89 – 1.85) |
59.26 – 1.92 (1.97 – 1.92) |
59.06 – 1.68 (1.71 – 1.68) |
59.08 – 1.68 (1.71 – 1.68) |
61.32 – 1.66 (1.69 – 1.66) |
| Total number of observed reflections | 313354 (19367) | 282012 (13838) | 240304 (12262) | 240032 (12417) | 263601 (13719) |
| Number of unique reflections | 24681 (1516) | 22592 (1272) | 33408 (1685) | 33411 (1701) | 37045 (1856) |
| Rmerge (%)b | 7.5 (92.2) | 15.9 (93.3) | 7.7 (93.4) | 6.9 (105.5) | 17.5 (85.2) |
| Rpim (%)c | 2.2 (26.4) | 4.8 (28.7) | 3.1 (37.2) | 2.8 (41.7) | 7.1 (33.5) |
| CC1/2 (%) | 0.99 (0.94) | 0.99 (0.75) | 0.99 (0.88) | 0.99 (0.89) | 0.99 (0.80) |
| < I/σ(I)>d | 13.2 (2.0) | 10.7 (3.1) | 14.5 (2.0) | 15.7 (1.9) | 8.2 (2.0) |
| Completeness (%) | 99.6 (99.8) | 99.0 (84.7) | 100 (99.9) | 99.8 (99.9) | 100 (100) |
| Multiplicity | 12.7 (12.8) | 12.5 (10.9) | 7.2 (7.3) | 7.2 (7.3) | 7.1 (7.4) |
| Wilson B-factor (Å2) | 37.9 | 21.1 | 23.5 | 22.7 | 13.6 |
| Refinement | |||||
| Rwork (%)e | 21.0 | 16.0 | 19.7 | 18.1 | 17.2 |
| Rfree (%)f | 25.0 | 20.1 | 23.6 | 22.3 | 20.2 |
| No. of atoms | 2458 | 2629 | 2495 | 2591 | 2766 |
| Protein atoms | 2346 | 2339 | 2339 | 2339 | 2371 |
| Ligand atoms | - | 12 | 13 | 14 | 35 |
| Solvent atoms | 112 | 278 | 143 | 238 | 360 |
| Model quality | |||||
| RMS deviation from ideal value | |||||
| Bond length (Å) | 0.006 | 0.010 | 0.010 | 0.009 | 0.009 |
| Bond angle (°) | 1.17 | 1.45 | 1.45 | 1.43 | 1.45 |
| Average B-factor | |||||
| Protein atoms (Å2) | 45.0 | 25.6 | 24.2 | 26.1 | 13.9 |
| Ligand atoms (Å2) | - | 37.1 | 26.4 | 35.4 | 28.5 |
| Waters (Å2) | 46.4 | 52.0 | 39.2 | 52.1 | 42.9 |
| Ramachandran plotg | |||||
| Most favored regions (%) | 95.4 | 95.7 | 95.4 | 95.7 | 95.4 |
| Allowed regions (%) | 4.6 | 4.3 | 4.6 | 4.3 | 4.6 |
| Outlier regions (%) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| PDB ID entry | 6OFZ | 6OI0 | 6OI1 | 6OI2 | 6OI3 |
Values in parentheses refer to the highest resolution shell.
Rmerge= (ΣhklΣi|Ii(hkl) - < I(hkl)>|)/ΣhklΣi<Ii(hkl)>, where Ii(hkl) is the intensity of the ith measurement of reflection (hkl) and < I(hkl) > is its mean intensity.
Rpim = (Σhkl[1/(Nhkl-1)]1/2Σi|Ii(hkl) - < I(hkl) >|) / ΣhklΣi<Ii(hkl)>, where Ii(hkl) is the intensity of the ith measurement of reflection (hkl), < I(hkl) > is its mean intensity and N is the number of measurements.
I is the integrated intensity and σ(I) is its estimated standard deviation.
Rwork = (Σhkl|Fo-Fc|)/ΣhklFo where Fo and Fc are the observed and calculated structure factors.
Rfree is calculated as for Rwork but from a randomly selected subset of the data (5%), which were excluded from the refinement calculation.
Calculated by MOLPROBITY