Neutron/X-ray crystal structure of AAC-VIa bound to kanamycin b
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6BBZ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | polyethylene glycol 8000, 0.2 M MgCl2, 0.1 M Tris, pH 8.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.62 | 53.05 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 51.359 | α = 90 |
| b = 86.058 | β = 93.98 |
| c = 77.597 | γ = 90 |
| Symmetry |
|---|
| Space Group | I 1 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2017-01-01 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | AREA DETECTOR | ORNL ANGER CAMERA | | 2017-01-01 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | | |
| 2 | NUCLEAR REACTOR | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.0-4.0 | ORNL Spallation Neutron Source | MANDI |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
|---|
| 1 | 2.3 | 50 | 93.4 | 0.061 | | | | | | 14.7 | 3 | | 13955 | | | |
| 2 | 2.3 | 14.08 | 85.2 | 0.148 | | | | | | 7.4 | 2.6 | | 12969 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.3 | 2.38 | | 0.347 | | | | | | 3.34 | 2.9 | |
| 2 | 2.3 | 2.38 | | 0.244 | | | | | | 2.8 | 1.93 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.3 | 14 | | | | 12859 | 638 | 86 | | 0.238 | 0.237 | 0.257 | Random | 53.27 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | | | | | | | | | | | | | | |
| Temperature Factor Modeling |
|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
|---|
| | | | | |
| | | | | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2027 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 70 |
| Heterogen Atoms | 34 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
