Joint X-ray/neutron structure of D132N Bacillus halodurans RNase H1 in the apo-form
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1ZBF | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 5 | 291 | 0.1 M NaOAc pH 5.0, 0.2 M (NH4)2SO4, and 20% PEG 3350 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.49 | 50.65 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 67.417 | α = 90 |
| b = 67.417 | β = 90 |
| c = 60.798 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 31 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | | 2024-02-28 | L | LAUE |
| 2 | 1 | x-ray | 293 | PIXEL | DECTRIS EIGER R 4M | | 2024-03-01 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | NUCLEAR REACTOR | ORNL High Flux Isotope Reactor BEAMLINE CG4D | 2.8-4.5 | ORNL High Flux Isotope Reactor | CG4D |
| 2 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
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 | 2.4 | 41.74 | 81.3 | 0.143 | | | 0.056 | 0.968 | | 5.7 | 5.6 | | 5059 | | | |
| 2 | 2.2 | 60.8 | 95 | 0.14 | | | 0.076 | 0.984 | | 8.3 | 4.3 | | 8440 | | | |
| 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 | 2.4 | 2.53 | | 0.326 | | | 0.156 | 0.736 | | 2.4 | 4 | |
| 2 | 2.2 | 2.28 | | 0.663 | | | 0.355 | 0.554 | | 1.2 | 4.4 | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.4 | 40 | | 2.5 | | 4337 | 219 | 68.4 | | | 0.241 | | 0.256 | | | 35.84 |
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.2 | 40 | | 2.5 | | 6765 | 338 | 80.4 | | | 0.204 | 0.3334 | 0.234 | 0.3448 | random | 35.84 |
| 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] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| x_torsion_deg | 23.8 |
| x_torsion_deg | 23.8 |
| x_angle_deg | 1 |
| x_angle_deg | 1 |
| x_torsion_impr_deg | 0.75 |
| x_torsion_impr_deg | 0.75 |
| x_bond_d | 0.008 |
| x_bond_d | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1092 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 48 |
| Heterogen Atoms | 5 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| LAUEGEN | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
| nCNS | refinement |
