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 |
