Joint X-ray/neutron structure of wild-type 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 |
|---|
| 2.48 | 50.34 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 67.201 | α = 90 |
| b = 67.201 | β = 90 |
| c = 60.814 | 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 | POSITION SENSITIVE DETECTOR | ORNL ANGER CAMERA | | 2023-07-05 | L | LAUE |
| 2 | 1 | x-ray | 293 | PIXEL | DECTRIS EIGER R 4M | | 2023-07-06 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2-4.16 | ORNL Spallation Neutron Source | MANDI |
| 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 | 2.48 | 14.7 | 95.5 | 0.201 | | | 0.096 | 0.95 | | 7.6 | 4.6 | | 5519 | | | |
| 2 | 1.9 | 60.8 | 99.6 | 0.058 | | | 0.023 | 0.997 | | 25 | 7.4 | | 12840 | | | |
| 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 | 2.48 | 2.57 | | 0.233 | | | 0.131 | 0.295 | | 2.8 | 3.6 | |
| 2 | 1.9 | 1.97 | | 0.663 | | | 0.297 | 0.623 | | 1.6 | 5.5 | |
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 | 2.48 | 14.7 | | 2.5 | | 5519 | 305 | 93.8 | | | 0.279 | | 0.311 | | random | 35.69 |
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 40 | | 2.5 | | 11690 | 609 | 90.8 | | | 0.219 | 0.3472 | 0.226 | 0.3435 | random | 35.69 |
| 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 | 19.5 |
| x_torsion_deg | 19.5 |
| x_angle_deg | 1.1 |
| x_angle_deg | 1.1 |
| x_torsion_impr_deg | 0.77 |
| x_torsion_impr_deg | 0.77 |
| 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 | 59 |
| Heterogen Atoms | 5 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| Mantid | data reduction |
| LAUENORM | data scaling |
| PHASER | phasing |
