Table 1.
Crystallographic Refinement Statistics
| 1 L. Lactis IrHex |
2 L. lactis |
3 L. lactis high [Mn2+] (Mn edge) |
4 L. lactis high [Mn2+] (below Mn edge) |
5 L. lactis low [Mn2+] (Mn edge) |
6 L. lactis A41U (Sr edge) |
7 E. coli apo (Sr edge) |
8 E. coli apo (Sr inflection) |
9 E. coli apo (Sr remote) |
|
|---|---|---|---|---|---|---|---|---|---|
| Data Collection | |||||||||
| Beamline | APS 24 ID-C | CHESS A1 | APS 24 ID-C | APS 24 ID-C | APS 24 ID-C | APS 24 ID-C | APS 24 ID-C | APS 24 ID-C | APS 24 ID-C |
| Wavelength (Å) | 1.1049 | 0.979 | 1.8923 | 1.9252 | 1.892 | 0.769 | 0.769 | 0.7692 | 0.9999 |
| Resolution range (Å) | 64.58–3.12 (3.22–3.12) | 50.0 – 3.10 (3.15–3.10) | 116.1–2.81 (2.91–2.81) | 116.3–3.31 (3.43–3.31) | 55.9–2.85 (2.95–2.85) | 47.4–2.24 (2.32–2.24) | 123.6–3.07 (3.24–3.07) | 123.29–3.03 (3.19–3.03) | 123.6–3.0 (3.11–3.0) |
| Space group | C 1 2 1 | C 1 2 1 | C 1 2 1 | C 1 2 1 | C 1 2 1 | P 1 | R 3 2 :H | R 3 2 :H | R 3 2 :H |
| Unit cell (a, b, c, α, β, γ) | 67.0, 129.2, 114.1 90, 91.7, 90 |
67.3, 129.2,115.8 90, 93.1, 90 |
67.3, 129.2, 115.8 90, 93.1, 90 |
67.8, 129.7, 116.5 90, 93.5, 90 |
67.3, 127.9, 115.3 90 93.37 90 |
50.4, 62.5, 70.0 116.2, 101.8, 98.8 |
159.4 159.4 277.4 90 90 120 |
158.9, 158.9, 277.3 90 90 1 20 |
159.4 159.4 277.1 90 90 120 |
| Total reflections | 76933 (14342) | 334008 (5130) | 80142 (10778) | 49478 (7216) | 86315 (8601) | 102574 (10543) | 292002 (43787) | 300381 (45331) | 310763 (31582) |
| Unique reflections | 17204 (3128) | 17922 (922) | 21167 (671) | 14408 (1361) | 20952 (2074) | 32334 (3300) | 25625 (3674) | 26469 (3802) | 27410 (2711) |
| Multiplicity | 4.5 (4.6) | 5.4 (5.8) | 3.5 (3.5) | 3.4 (2.4) | 4.1 (4.1) | 3.2 (3.2) | 11.4 (11.9) | 11.2 (11.9) | 11.3 (11.6) |
| Completeness (%) | 99.3 (99.2) | 96.4 (98.9) | 93.6 (89.1) | 95.81 (91.47) | 92 (92) | 90. (95) | 99.9 (99.9) | 99.9 (99.9) | 100.0 (100.0) |
| Mean I/sigma(I) | 12.7 (3.2) | 6.82 (1.52) | 5.49 (0.90) | 4.03 (0.71) | 20.5 (2.87) | 17.6 (2.10) | 9.8 (0.9) | 13.1 (1.1) | 20.2 (2.41) |
| Wilson B-factor (Å2) | 81.60 | 44.48 | 69.00 | 98.80 | 65.44 | 55.05 | 73.19 | 99.56 | 93.34 |
| R-merge | 0.159 (0.649) | 0.133 (0.610) | 0.144 (2.35) | 0.194 (1.60) | 0.136 (0.470) | 0.053 (0.550) | 0.138 (2.992) | 0.115 (2.37) | 0.116 (1.01) |
| R-meas | 0.181 (0.733) | 0.141 | 0.170 (2.784) | 0.231 (1.90) | 0.157 (0.539) | 0.0647 (0.662) | 0.151 (3.27) | 0.121 (2.48) | 0.122 (1.05) |
| CC1/2 | 0.976 (0.849) | - | 0.990 (0.565) | 0.988 (0.573) | 0.963 (0.945) | 0.992 (0.722) | 0.998 (0.777) | 0.968 (0.960) | 0.957 (0.943) |
| Refinement | |||||||||
| Reflections used in refinement | 21166 (669) | 14406 (1364) | 20887 (2058) | 31358 (3043) | 27328 (2703) | ||||
| Reflections used for R-free | 2074 (53) | 1430 (127) | 2030 (206) | 1741 (171) | 1738 (172) | ||||
| R-work | 0.207 (0.434) | 0.223 (0.410) | 0.192 (0.393) | 0.198 (0.336) | 0.214 (0.324) | ||||
| R-free | 0.247 (0.485) | 0.256 (0.488) | 0.223 (0.428) | 0.241 (0.417) | 0.246 (0.376) | ||||
| Total non-hydrogen atoms | 4464 | 4459 | 4451 | 4629 | 4130 | ||||
| -macromolecules | 4330 | 4330 | 4284 | 4280 | 3919 | ||||
| -Ligands | 59 | 66 | 111 | 140 | 139 | ||||
| RMS (bonds, Å) | 0.002 | 0.001 | 0.010 | 0.006 | 0.010 | ||||
| RMS (angles, °) | 0.52 | 0.39 | 0.46 | 1.03 | 0.73 | ||||
| Clash score | 2.59 | 3.19 | 3.19 | 5.30 | 4.46 | ||||
| Average B-factor (Å2) | 84.60 | 88.70 | 71.46 | 57.40 | 127.26 | ||||
| -macromolecules | 84.30 | 88.40 | 70.48 | 55.67 | 126.35 | ||||
| -ligands | 117.60 | 112.80 | 108.89 | 95.31 | 164.86 | ||||
| -solvent | 78.50 | 80.80 | 72.65 | 67.50 | 104.14 |
*
Where applicable, statistics for the highest-resolution shell are shown in parentheses.
*
Friedel pairs were averaged when calculating reflection statistics.
*
Dataset #2 was used for building an initial model, but is not shown in any figures in this study. All dataset resolutions were extended at most to shells for which CC1/2 > 0.5. Datasets used for final model refinement (bold: 5, 6, and 9) were further limited based on I/sigma(I).
*
Datasets 3 and 4 were used to produce anomalous difference maps at and below the Mn edge.