Table 3.
Summary of Crystallization Conditions and Data Collection, Processing, and Refinement Statistics for Deposited Structures of SmGhrBa
| SmGhrB PDB ID | 5v7n | 5v7g | 5v6q | 5j23 | 5uog | 5v72 |
| Complex | NADP+ and 2-keto-D-gluconic acid | NADPH and oxalate | NADP+ and malonate | 2-phospho-AD PR | apo unliganded | apo citrate |
| Diffraction images DOI | 10.18430/M35V7N | 10.18430/M35V7G | 10.18430/M35V6Cb | 10.18430/M35J23 | 10.18430/M35UOG | 10.18430/M35V72 |
| Crystallization | ||||||
| protein stock cone. (mg/mL) | 13.2 | 13.2 | 13.2 | 13.2 | 13.2 | 13.2 |
| ligands added | 5 mM NADP+ 100 mM 2-keto- D-gluconic acid hemicalcium salt, pH 7.0 | 5 mM NADPH 50 mM oxalic acid, pH 7.0 | 5 mM NADP+ | 5 mM NADPH 50 mM glycolic acid | 5 mM NADPH | none |
| protease added | rTEV | rTEV | rTEV | rTEV | none | chymotrypsin |
| precipitant mix | 0.2 M magnesium formate pH = 5.9, 20% w/v PEG 3350 (TOP96 #24) | 0.1 M sodium cacodylate pH = 6.5, 18% w/v PEG 8000, 0.2 M sodium acetate (TOP96 #41) | 1.1 M malonic acid, 0.072 M succinic acid, 0.15 M ammonium citrate tribasic, 0.18 M DL-malic acid, 0.096 M ammonium tartrate dibasic, 0.24 M sodium acetate, 0.3 M sodium formate, pH = 7.0 (MCSG suite 2 #20) | 0.1 M citric acid pH = 3.5, 2 M ammonium sulfate, (MCSG suite 3 #61) | 0.1 M sodium citrate pH 20% w/v PEG 6000 (MCSG suite 2 #9) | |
| cryoprotection | drying over 1 M sodium chloride | drying over 1 M sodium chloride | paratone-N | drying over 1 M sodium chloride | 20% ethylene glycol | air-drying |
| Data Processing | ||||||
| resolution (Å) | 50.00–1.75 (1.78–1.75) | 50.00–1.75 (1.78–1.75) | 50.00–1.95 (1.98–1.95) | 50.00–2.30 (2.34–2.30) | 50.00–2.40 (2.44–2.40) | 50.00–2.10 (2.14–2.10) |
| beamline | 21-ID-F | 21-ID-G | 21-ID-G | 21-ID-G | 19-ID | 21-ID-G |
| wavelength (Å) | 0.979 | 0.979 | 0.979 | 0.979 | 0.979 | 0.979 |
| space group | H3 | H3 | H3 | H3 | H3 | P2l |
| unit cell: a, b, c (Å) | 175.9, 175.9, 135.3 | 178.2, 178.2, 133.8 | 176.5, 176.5, 135.5 | 175.7, 175.7, 136.7 | 176.6, 176.6, 135.0 | 63.2, 157.9, 64.8 |
| protein chains in the asymmetric unit | 4 | 4 | 4 | 4 | 4 | 4 |
| completeness (%) | 99.6 (100.0) | 98.8 (99.7) | 99.6 (98.6) | 100.0 (100.0) | 100.0 (100.0) | 98.4 (99.1) |
| number of unique reflections | 156 897 | 157 652 | 114 355 | 70 083 | 61 899 | 68 211 |
| redundancy | 4.9 (4.9) | 4.5 (4.3) | 4.6 (4.5) | 3.9 (3.9) | 3.2 (3.2) | 3.2 (3.2) |
| ⟨I⟩/⟨σ(I)⟩ | 19.8 (1.8) | 17.9 (2.1) | 22.8 (2.1) | 18.2 (1.8) | 22.7 (2.0) | 12.5 (2.3) |
| CC1/2 - highest resolution shell | (0.61) | (0.78) | (0.69) | (0.68) | (0.69) | (0.79) |
| Rmerge | 0.113 (0.878) | 0.081 (0.667) | 0.105 (0.691) | 0.077 (0.662) | 0.061 (0.630) | 0.096 (0.431) |
| Wilson B factor (Å2) | 28.1 | 26.4 | 30.2 | 45.8 | 56.9 | 28.0 |
| Structure Refinement | ||||||
| Rwork/Rfree | 0.144/0.167 | 0.150/0.180 | 0.144/0.157 | 0.146/0.169 | 0.136/0.190 | 0.164/0.204 |
| mean ADP value (Å2) | 33 | 31 | 34 | 47 | 58 | 35 |
| number of protein atoms | 9511 | 9448 | 9446 | 9454 | 9325 | 9327 |
| mean ADP for protein (Å2) | 32 | 30 | 34 | 47 | 58 | 35 |
| number of water molecules | 1350 | 1809 | 841 | 603 | 972 | 1151 |
| mean ADP for water (Å2) | 41 | 41 | 39 | 46 | 54 | 40 |
| median ADP (occupancy) of the ligand in the active site, by chain | 26 (1), 28 (1), 35 (1), 38 (l) | 28 (0.8), 23 (0.7), 18 (0.8), 25 (l.O) | 33 (1), 28 (1), 30 (1), 26 (1) | – | – | –, –, 33 (1), – |
| bond lengths rmsd (Å) | 0.011 | 0.011 | 0.009 | 0.013 | 0.009 | 0.015 |
| Structure Refinement | ||||||
| bond angles rmsd (deg) | 1.5 | 1.5 | 1.3 | 1.5 | 1.3 | 1.5 |
| rotamer outliers (%) | 0.80 | 0.5 | 0.51 | 0.60 | 1.04 | 1.24 |
| Ramachandran outliers (%) | 0.32 | 0.32 | 0.08 | 0.32 | 0.00 | 0.00 |
| Ramachandran favored (%) | 97.31 | 97.4 | 97.4 | 97.9 | 97.5 | 98.2 |
| clashscore/clashscore percentile (%) | 0.51/100 | 0.31/100 | 0.41/100 | 0.87/1000 | 0.69/100 | 0.69/100 |
| MolProbity score | 0.81 | 0.73 | 0.77 | 0.80 | 0.83 | 0.80 |
a
Data prepared as for Table 2.