Table 1.
Crystallographic Data for BfrB Structures.
| As isolated (N148L) |
Fe-soaked (N148L) |
As isolated (Q151L) |
Fe-soaked (Q151L) |
As-isolated (D34F) |
Fe-soaked (D34F) |
As-isolated (C89S/K96C) |
As-isolated-2 (C89S/K96C) |
Fe-soaked (C89S/K96C) |
|
|---|---|---|---|---|---|---|---|---|---|
| Data Collection | |||||||||
| Unit-cell parameters (Å, º) | a=125.73 | a=125.32 | a=125.67 | a=125.59 | a=125.68 | a=125.49 | a=b=158.57 | a=b=155.13 | a=b=153.99 |
| b=203.35 | b=203.29 | b=203.15 | b=203.22 | b=203.54 | b=203.40 | c=152.38 | c=155.18 | c=155.20 | |
| c=208.27 | c=207.18 | c=207.79 | c=207.40 | c=206.97 | c=207.25 | ||||
| Space group | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P6322 | P6322 | P6322 |
| Resolution (Å)1 | 49.39-2.00 (2.03-2.00) | 49.36-1.95 (1.98-1.95) | 49.24-1.95 (1.98-1.95) | 49.35-2.25 (2.29-2.25) | 49.41-2.05 (2.09-2.05) | 49.39-2.20 (2.24-2.20) | 49.13-1.65 (1.68-1.65) | 48.27-1.80 (1.83-1.80) | 48.23-1.80 (1.83-1.80) |
| Wavelength (Å) | 1.74013 | 1.74013 | 1.00000 | 1.73964 | 1.00000 | 1.73769 | 1.00000 | 1.00000 | 1.73963 |
| Temperature (K) | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
| Observed reflections | 2,270,196 | 3,760,949 | 2,639,550 | 1,749,112 | 2,240,862 | 1,490,791 | 2,688,900 | 2,015,697 | 1,825,740 |
| Unique reflections | 356,578 | 373,157 | 384,285 | 250,626 | 328,340 | 257,692 | 134,788 | 101,666 | 99,837 |
| <I/σ(I)>1 | 10.8 (1.7) | 14.7 (2.2) | 10.8 (2.2) | 12.2 (2.4) | 13.1 (2.2) | 18.1 (3.4) | 12.3 (2.3) | 20.8 (2.3) | 22.3 (1.8) |
| Completeness (%)1 | 99.7 (94.1) | 97.7 (91.5) | 100 (100) | 100 (100) | 99.5 (98.9) | 96.3 (71.8) | 100 (99.9) | 100 (100) | 99.7 (96.5) |
| Multiplicity1 | 6.4 (4.7) | 10.1 (8.1) | 6.9 (6.4) | 7.0 (6.7) | 6.8 (6.6) | 5.8 (2.4) | 19.9 (20.3) | 19.8 (19.2) | 18.3 (10.2) |
| Rmerge (%)1, 2 | 12.1 (81.5) | 14.0 (92.9) | 14.4 (95.8) | 14.4 (96.7) | 11.7 (95.1) | 6.2 (25.9) | 16.8 (179.1) | 10.6 (160.0) | 12.1 (131.3) |
| Rmeas (%)1, 4 | 13.2 (91.6) | 14.8 (99.1) | 15.6 (103.3) | 15.2 (104.8) | 12.6 (103.1) | 7.4 (35.6) | 17.7 (188.2) | 10.9 (164.3) | 12.4 (138.3) |
| Rpim (%)1, 4 | 5.2 (40.8) | 4.6 (33.6) | 5.9 (40.9) | 5.7 (40.3) | 4.8 (39.7) | 2.4 (21.4) | 3.9 (41.2) | 2.4 (37.2) | 2.8 (42.7) |
| CC1/21, 5 | 0.996 (0.609) | 0.996 (0.712) | 0.996 (0.695) | 0.996 (0.680) | 0.998 (0.710) | 0.998 (0.885) | 0.997 (0.783) | 1.000 (0.818) | 0.999 (0.701) |
| Refinement | |||||||||
| Resolution (Å) | 49.39-2.00 | 49.36-1.95 | 49.34-1.95 | 49.35-2.25 | 41.06-2.05 | 48.39-2.20 | 38.10-1.65 | 37.27-1.80 | 48.23-1.80 |
| Reflections (working/test)6 | 654,121/34,746 | 688,869/36,492 | 364,760/19,327 | 461,135/24,449 | 311,642/16,559 | 485,422/24,416 | 127,956/6,770 | 96,523/5,074 | 180,676/9,520 |
| Rfactor / Rfree (%)3 | 16.9/21.1 | 15.5/19.3 | 15.6/18.8 | 15.4/19.2 | 15.3/19.2 | 14.9/18.7 | 14.5/16.2 | 15.3/17.8 | 14.7/17.2 |
| No. of atoms (Protein/Heme/K+/Iron/Sulfate/Water) | 30,466/1,032/6/0/0/2,588 | 30,665/1,032/6/126/40/3,005 | 30,252/5160/0/0/2,998 | 30,343/516/0/120/40/2,110 | 30,434/516/6/0/0/2,066 | 30,262/516/6/144/40/2,278 | 5,151/172/1/0/0/762 | 5,151/172/1/0/8/641 | 5,165/172/1/37/8/748 |
| Model Quality | |||||||||
| R.m.s deviations | |||||||||
| Bond lengths (Å) | 0.010 | 0.956 | 0.009 | 0.011 | 0.016 | 0.010 | 0.008 | 0.010 | 0.009 |
| Bond angles (º) | 0.975 | 0.017 | 1.008 | 1.023 | 1.265 | 0.985 | 1.107 | 0.996 | 1.013 |
| Average B-factor (Å2) | |||||||||
| All Atoms | 26.0 | 22.6 | 20.9 | 24.8 | 28.6 | 24.8 | 22.6 | 27.7 | 24.8 |
| Protein | 25.4 | 19.0 | 19.9 | 31.7 | 28.2 | 24.1 | 20.6 | 26.2 | 23.1 |
| Heme | 27.9 | 21.8 | 18.0 | 30.4 | 25.6 | 24.4 | 20.2 | 24.3 | 22.9 |
| K+ | 38.6 | 28.2 | - | - | 21.5 | 39.9 | 15.9 | 20.6 | 19.5 |
| Iron | - | 45.1 | - | 60.0 | - | 45.1 | - | - | 46.8 |
| Sulfate | - | 48.0 | - | 59.8 | - | 53.4 | - | 52.2 | 39.3 |
| Water | 32.9 | 20.0 | 29.5 | 39.3 | 35.7 | 31.2 | 34.0 | 38.8 | 35.4 |
| Coordinate error (maximum likelihood) (Å) | 0.24 | 0.19 | 0.17 | 0.22 | 0.20 | 0.20 | 0.15 | 0.17 | 0.18 |
| Ramachandran Plot | |||||||||
| Most favored (%) | 99.7 | 99.6 | 100 | 100 | 99.5 | 99.8 | 99.7 | 99.7 | 99.5 |
| Additionally allowed (%) | 0.3 | 0.4 | - | - | 0.5 | 0.2 | 0.3 | 0.3 | 0.5 |
| PDB Code | 4TO9 | 4TOA | 4TOB | 4TOC | 4TOD | 4TOE | 4TOF | 4TOG | 4TOH |
Values in parenthesis are for the highest resolution shell.
Rmerge = ΣhklΣi |Ii(hkl) - <I(hkl)>| /ΣhklΣi Ii(hkl), where Ii(hkl) is the intensity measured for the ith reflection and <I(hkl)> is the average intensity of all reflections with indices hkl.
Rfactor = Σhkl ‖Fobs (hkl) | - |Fcalc (hkl) ‖ / Σhkl |Fobs (hkl)|; Rfree is calculated in an identical manner using 5% of randomly selected reflections that were not included in the refinement.
Rmeas = redundancy-independent (multiplicity-weighted) Rmerge(32, 58). Rpim = precision-indicating (multiplicity-weighted) Rmerge(59, 60).
CC1/2 is the correlation coefficient of the mean intensities between two random half-sets of data (61, 62).
For the data sets obtained from iron soaked crystals or native data sets collected at the iron peak wavelength, the number of reflections used during refinement is greater than the number unique reflections reported for data scaling. This is due to the fact that Friedel pairs were kept separate during refinement and the anomalous scattering factors for the Fe2+ atoms were refined.