Joint Xray/neutron crystal structure determination of H-labeled perdeuterated rubredoxin at 295K
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1BRF | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 3.8 M sodium/potassium phosphate, hanging drop | |||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.2 | 44.1 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 34.238 | α = 90 |
| b = 35.096 | β = 90 |
| c = 43.858 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 295 | CCD | MARMOSAIC 225 mm CCD | 2008-03-09 | SINGLE WAVELENGTH | |||||||
| 2 | 1 | neutron | 295 | IMAGE PLATE | MAATEL LADI-III | LAUE | ||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0 | APS | 22-BM |
| 2 | NUCLEAR REACTOR | 3.1-4.2 | |||
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 | 1.1 | 27.4 | 21725 | ||||||||||||||||
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 | ||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.1 | 24.51 | 1.35 | 21691 | 1107 | 98.2 | 0.145 | 0.145 | 0.1422 | 0.156 | 0.1553 | 16.79 | ||||||
| NEUTRON DIFFRACTION | 1.66 | 27.4 | 1.09 | 4602 | 209 | 69.7 | 0.188 | 0.187 | 0.202 | ||||||||||
| 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] | |
| 0.82 | 0.296 | 0.425 | ||||
| -0.25 | 0.828 | 1.536 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 18.003 |
| f_angle_d | 1.426 |
| f_chiral_restr | 0.095 |
| f_bond_d | 0.014 |
| f_plane_restr | 0.011 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 414 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 37 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| LAUEGEN | data reduction |
