Joint X-ray/neutron structure of wild type MTAN complexed with SRH and adenine
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 3NM5 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 296 | PEG550 MME, 50 mM magnesium chloride hexahydrate, 100 mM HEPES, pH 7 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.7 | 54.53 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 83.189 | α = 90 |
| b = 83.189 | β = 90 |
| c = 67.633 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 32 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | neutron | 296 | IMAGE PLATE | CUSTOM-MADE | | 2013-01-15 | M | SINGLE WAVELENGTH |
| 2 | 1 | x-ray | 296 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2013-01-15 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | NUCLEAR REACTOR | OTHER | 2.66 | | |
| 2 | ROTATING ANODE | RIGAKU | 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 | 2.5 | 50 | 97.1 | 0.1 | | | | | | 11.5 | 3.9 | | 9393 | | | |
| 2 | 1.82 | 40 | 94 | 0.026 | | | | | | 43.1 | 4.4 | | 23011 | | | |
| 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 | 2.5 | 2.59 | | 0.681 | | | | | | 1.7 | 3.2 | |
| 2 | 1.82 | 1.89 | | 0.496 | | | | | | 2.9 | 4.5 | |
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 | 2.5 | 31.79 | | | 9655 | 7859 | 356 | 81.4 | | | 0.343 | | 0.376 | | | 31.49 |
| x-ray diffraction | MOLECULAR REPLACEMENT | 1.82 | 31.79 | | | 24544 | 20253 | 997 | 82.5 | | | 0.253 | | 0.257 | | | 31.49 |
| 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 | 19.7 |
| x_torsion_deg | 19.7 |
| x_torsion_impr_deg | 14.6 |
| x_torsion_impr_deg | 14.6 |
| x_angle_deg | 4.4 |
| x_angle_deg | 4.4 |
| x_bond_d | 0.129 |
| x_bond_d | 0.129 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1755 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 70 |
| Heterogen Atoms | 27 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| CNS | refinement |
| DENZO | data processing |
| SCALEPACK | data scaling |
| HKL-3000 | data processing |
| Coot | model building |
| O | model building |
| nCNS | refinement |
