Table 1 Structure data collection and refinement statistics
From: Structural basis of ECF-σ-factor-dependent transcription initiation
Structure | Mtb RPitc5-σL_sp4 | Mtb RPitc5-σL_sp5 | Mtb RPitc5-σL_sp6 |
PDB code | 6DV9 | 6DVB | 6DVC |
Data collection a | |||
Source | APS 19-ID | SSRL-9-2 | APS 19-ID |
Space group | P212121 | P212121 | P212121 |
Cell dimensions | |||
a, b, c (Å) | 143.3, 161.4, 237.7 | 143.7, 160.6, 240.4 | 146.3, 161.5, 240.6 |
α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
Resolution (Å) | 50.0–3.8 (3.9–3.8) | 50.0-3.8 (3.9–3.8) | 50.0-3.3 (3.4–3.3) |
Number of unique reflections | 53,020 | 53,728 | 98,083 |
R merge b | 0.162 (0.567) | 0.188 (0.706) | 0.175 (0.710) |
R meas | 0.172 (0.613) | 0.200 (0.752) | 0.184 (0.764) |
R pim | 0.056 (0.222) | 0.066 (0.246) | 0.055 (0.273) |
CC1/2 (highest resolution shell) | 0.526 | 0.715 | 0.558 |
I/σI | 8.6 (2.2) | 7.3 (1.9) | 13 (1.9) |
Completeness (%) | 96.6 (90.5) | 97.1 (96.5) | 98.9 (99.3) |
Redundancy | 10.7 (9.9) | 8.2 (8.1) | 10.4 (7.4) |
Anomalous completeness (%) | N/A | N/A | N/A |
Anomalous redundancy | N/A | N/A | N/A |
Refinement a | |||
Resolution (Å) | 50.0–3.8 | 50.0–3.8 | 50.0–3.3 |
Number of unique reflections | 52,512 | 53,617 | 85,687 |
Number of test reflections | 2625 | 2691 | 4267 |
Rwork/Rfree | 0.18/0.23 (0.29/0.32) | 0.20/0.24 (0.32/0.35) | 0.19/0.23 (0.34/0.35) |
Number of atoms | |||
Protein | 24,956 | 24,974 | 24,982 |
Ligand/ion | 3 | 2 | 2 |
r.m.s. deviations | |||
Bond lengths (Å) | 0.002 | 0.002 | 0.002 |
Bond angles (°) | 0.489 | 0.457 | 0.468 |
MolProbity statistics | |||
Clash score | 7.2 | 6.3 | 6.0 |
Rotamer outliers (%) | 1.6 | 2.4 | 2.6 |
Cβ outliers (%) | 0 | 0 | 0 |
Ramachandran plot | |||
Favored (%) | 95.2 | 95.4 | 95.5 |
Outliers (%) | 0.3 | 0.2 | 0.3 |
Structure | Mtb [BrU]RPo-σL_sp6 | Mtb [SeMet15,76]RPo-σL_sp6 |
PDB code | 6DVD | 6DVE |
Data collection a | ||
Source | APS 19-ID | APS 19-ID |
Space group | P212121 | P212121 |
Cell dimensions | ||
a, b, c (Å) | 142.1, 161.5, 239.4 | 142.8, 160.6, 240.2 |
α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
Resolution (Å) | 50.0–3.9 (4.0–3.9) | 50.0–3.8 (3.9–3.8) |
Number of unique reflections | 44,608 | 50,281 |
R merge b | 0.110 (0.768) | 0.178 (>1.000) |
R meas | 0.121 (0.847) | 0.187 (>1.000) |
R pim | 0.047 (0.348) | 0.062 (0.608) |
CC1/2 (highest resolution shell) | 0.797 | 0.589 |
I/σI | 14.3 (1.6) | 10.2 (1.0) |
Completeness (%) | 87.4 (68.5) | 92.1 (79.3) |
Redundancy | 6.0 (4.8) | 9.3 (5.5) |
Anomalous completeness (%) | 87.4 | 92.1 |
Anomalous redundancy | 6.0 | 9.3 |
Refinement a | ||
Resolution (Å) | 45.9–3.9 | 46.7–3.8 |
Number of unique reflections | 37,593 | 40,877 |
Number of test reflections | 1996 | 1987 |
Rwork/Rfree | 0.22/0.24 (0.25/0.26) | 0.20/0.24 (0.25/0.30) |
Number of atoms | ||
Protein | 24,743 | 24,782 |
Ligand/ion | 2 | 4 |
r.m.s. deviations | ||
Bond lengths (Å) | 0.002 | 0.002 |
Bond angles (°) | 0.491 | 0.492 |
MolProbity statistics | ||
Clash score | 6.6 | 6.8 |
Rotamer outliers (%) | 2.6 | 1.7 |
Cβ outliers (%) | 0 | 0 |
Ramachandran plot | ||
Favored (%) | 95.3 | 95.0 |
Outliers (%) | 0.3 | 0.3 |
