Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Z-DNA (X-ray)
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION | 5.6 | 293 | 0.01M Magnesium Acetate
0.05M MES pH 5.6
2.5M Ammonium Sulfate, VAPOR DIFFUSION, temperature 293K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 1.76 | 30.3 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 17.9 | α = 90 |
| b = 30.59 | β = 90 |
| c = 44.61 | 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 | 293 | CCD | RIGAKU SATURN 92 | | 2006-01-01 | M | SINGLE WAVELENGTH |
| 2 | 1 | 293 | AREA DETECTOR | | | 2006-01-01 |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU FR-E DW | 1.54 | | |
| 2 | NUCLEAR REACTOR | | 0.6-0.7 | | |
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 | 1.53 | 100 | 92.1 | | | | | | | | | 3696 | 3696 | | | |
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 | 1.53 | 100 | | | 3696 | 3696 | 178 | | | | 0.1937 | 0.19 | 0.2359 | 0.18 | random, throughout | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.4 | 100 | | | 4680 | 4680 | 240 | | | | 0.3007 | | 0.3147 | | random, throughout | |
| 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] |
|---|
| | | | | |
| | | | | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | |
| Nucleic Acid Atoms | 240 |
| Solvent Atoms | 41 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| CrystalClear | data collection |
| PHASER | phasing |
| nCNS-TINKER | refinement |
| d*TREK | data reduction |
| SCALA | data scaling |
