Table 1. Crystallographic statistics for multitemperature and mutant X-ray datasets.
Overall statistics given first (statistics for highest-resolution bin in parentheses). For WT apo, 100 K: statistics are taken from our remodeled structure where appropriate, or from the original PDB ID 1sug when possible otherwise, or given as ‘---” where unavailable.
Table 1—source data 1. Multiconformer models best explain PTP1B X-ray data across temperatures.
R-factors are reported for the deposited multiconformer models for multitemperature datasets in Table 1 vs. single-conformer models derived by removing alternative conformations and re-refining with Phenix either with default parameters (‘without solvent picking’) or with automated water placement turned on by adding the flag ‘ordered_solvent = True’ (‘with solvent picking’) for 12 macro-cycles. For the new single-conformer models, R-factors are given both for state A with state B’s alternative conformations removed, and for state B with state A’s alternative conformations removed, to confirm that either option for a single-conformer model is worse than a multiconformer model. Overall, regardless of the choice of solvent parameters, at each temperature the multiconformer model has lower (better) Rwork and Rfree.
elife-36307-table1-data1.txt (576B, txt)
DOI: 10.7554/eLife.36307.011
| WT apo, 100 K | WT* apo, 180 K | WT* apo, 240 K | WT* apo, 278 K | WT* with BB3, 278 K | K197C apo, 100 K | K197C tethered to 2, 100 K | |
|---|---|---|---|---|---|---|---|
| PDB ID | 6B90 | 6B8E | 6B8T | 6B8X | 6B8Z | 6BAI | 6B95 |
| Number of crystals used | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Wavelength (Å) | 0.8110 | 1.115869 | 1.115869 | 0.9795 | 1.11583 | 1.11583 | 1.11583 |
| Resolution range (Å) | 33.60–1.95 (2.02–1.95) | 19.18–1.82 (1.89–1.82) | 62.54–1.85 (1.92–1.85) | 31.31–1.74 (1.80–1.74) | 43.88–1.8 (1.86–1.8) | 75.57–1.95 (2.02–1.95) | 43.98–1.95 (2.02–1.95) |
| Space group | P 31 2 1 | P 31 2 1 | P 31 2 1 | P 31 2 1 | P 31 2 1 | P 31 2 1 | P 31 2 1 |
| Unit cell (Å, °) |
88.12 88.12 103.90 90 90 120 | 88.57 88.57 104.32 90 90 120 | 89.44 89.44 106.00 90 90 120 |
89.52 89.52 106.25 90 90 120 | 89.65 89.65 106.39 90 90 120 | 87.27 87.27 104.10 90 90 120 | 87.96 87.96 104.63 90 90 120 |
| Total reflections | --- | 339461 (33574) | 256701 (25484) | 299041 (30678) | 771858 (76158) | 653798 (63759) | 170094 (16845) |
| Unique reflections | 34486 (3371) | 42866 (4223) | 42343 (4156) | 50486 (4960) | 46311 (4561) | 33409 (3296) | 34596 (3387) |
| Multiplicity | 7.4 (---) | 7.9 (7.9) | 6.1 (6.1) | 5.9 (6.2) | 16.7 (16.7) | 19.6 (19.3) | 4.9 (5.0) |
| Completeness (%) | 99.9 (100.0) | 99.9 (100.0) | 100.0 (100.0) | 99.0 (98.3) | 100.0 (100.0) | 98.06 (98.51) | 99.81 (99.88) |
| Mean I/sigma(I) | 26.4 (4.4) |
21.40 (1.46) | 15.89 (1.46) | 17.15 (1.49) | 11.69 (0.75) | 25.06 (0.94) | 12.04 (0.81) |
| Wilson B (Å2) | 24.12 | 23.69 | 28.48 | 19.48 | 34.96 | 46.3 | 38.82 |
| Rmerge | 0.073 (0.515) | 0.089 (1.483) | 0.079 (1.215) | 0.098 (1.209) | 0.148 (2.664) | 0.076 (3.056) | 0.088 (1.852) |
| Rmeas | --- | 0.096 (1.585) | 0.086 (1.329) | 0.108 (1.318) | 0.153 (2.748) | 0.078 (3.138) | 0.098 (2.071) |
| Rpim | --- | 0.034 (0.556) | 0.035 (0.535) | 0.044 (0.520) | 0.038 (0.672) | 0.018 (0.705) | 0.044 (0.916) |
| CC1/2 | --- | 0.999 (0.520) | 0.999 (0.560) | 0.999 (0.496) | 0.997 (0.366) | 1.000 (0.438) | 0.999 (0.292) |
| CC* | --- | 1.000 (0.827) | 1.000 (0.847) | 1.000 (0.814) | 0.999 (0.732) | 1.000 (0.781) | 1.000 (0.672) |
| Reflections used in refinement | 34486 (3371) | 42862 (4223) | 42343 (4156) | 50486 (4959) | 46309 (4561) | 33302 (3296) | 34576 (3386) |
| Reflections used for Rfree | 1356 (128) | 1689 (165) | 1669 (163) | 1993 (196) | 1820 (176) |
1310 (135) |
1362 (135) |
| Rwork | 0.1580 (0.1881) | 0.1708 (0.2781) | 0.1674 (0.2760) | 0.1752 (0.3511) | 0.1675 (0.3116) | 0.2061 (0.3365) | 0.1858 (0.3295) |
| Rfree | 0.1926 (0.2090) | 0.1997 (0.2911) | 0.2123 (0.2869) | 0.2059 (0.3888) | 0.1978 (0.3017) | 0.2569 (0.3292) | 0.2307 (0.3686) |
| CCwork | --- | 0.963 (0.753) | 0.958 (0.789) | 0.964 (0.673) | 0.964 (0.709) | 0.934 (0.618) | 0.957 (0.574) |
| CCfree | --- | 0.948 (0.744) | 0.908 (0.677) | 0.948 (0.739) | 0.961 (0.757) | 0.994 (0.484) | 0.938 (0.294) |
| Non-H atoms | 2997 | 3021 | 3149 | 3260 | 2709 | 2502 | 2541 |
| Macromolecule atoms | 2657 | 2687 | 2875 | 3011 | 2460 | 2377 | 2370 |
| Ligand atoms | 46 | 40 | 34 | 24 | 82 | 16 | 36 |
| Solvent atoms | 294 | 294 | 240 | 225 | 167 | 109 | 135 |
| Protein residues | 298 | 298 | 299 | 298 | 289 | 282 | 285 |
| RMS bonds (Å) | 0.010 | 0.011 | 0.011 | 0.012 | 0.011 | 0.015 | 0.013 |
| RMS angles (°) | 1.01 | 1.02 | 1.10 | 1.08 | 1.14 | 1.30 | 1.15 |
| Ramachandran favored (%) | 97.64 | 97.64 | 97.98 | 95.95 | 97.19 | 95.00 | 95.76 |
| Ramachandran allowed (%) | 2.03 | 2.03 | 1.68 | 3.72 | 2.11 | 4.64 | 2.83 |
| Ramachandran outliers (%) | 0.34 | 0.34 | 0.34 | 0.34 | 0.70 | 0.36 | 1.41 |
| Rotamer outliers (%) | 1.35 | 2.67 | 1.87 | 2.38 | 2.19 | 6.44 | 4.91 |
| Clashscore | 2.79 | 3.31 | 3.62 | 2.98 | 2.79 | 6.06 | 3.36 |
| MolProbity score | 1.24 | 1.52 | 1.36 | 1.65 | 1.47 | 2.29 | 1.95 |
| Average B (Å2) | 29.35 | 30.22 | 36.50 | 28.06 | 43.58 | 55.81 | 49.66 |
| Average B, macromolecule (Å2) | 28.14 | 29.11 | 35.51 | 27.01 | 43.30 | 56.02 | 49.53 |
| Average B, ligands (Å2) | 47.43 | 48.08 | 60.29 | 67.33 | 41.13 | 45.41 | 53.91 |
| Average B, solvent (Å2) | 37.46 | 37.90 | 44.96 | 38.01 | 48.96 | 52.76 | 50.82 |