Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2GUB | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 5.9 | 280 | crystals grew with ammonium sulfate as a precipitant at pH of 5.9, batch crystallization, temperature 280K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.78 | 55.76 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 93.908 | α = 90 |
| b = 99.503 | β = 90 |
| c = 102.971 | γ = 90 |
| Symmetry |
|---|
| Space Group | I 2 2 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | neutron | 293 | AREA DETECTOR | position sensitive He3 | | 2010-09-15 | L | TOF LAUE |
| 2 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2010-06-14 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | NUCLEAR REACTOR | LANSCE BEAMLINE PCS | 0.6-7.0 | LANSCE | PCS |
| 2 | ROTATING ANODE | RIGAKU FR-E+ DW | 1.5418 | | |
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 | 28.46 | 86.9 | 0.225 | | | | | | 4.5 | 3 | 28290 | 28290 | 2.2 | 1.5 | |
| 2 | 1.7 | 29.86 | 99.2 | 0.077 | | | | | | 8.6 | 3.222 | 53087 | 53087 | | | |
| 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 | 2.11 | | 0.385 | 0.385 | | | | | 1.3 | 1.7 | |
| 2 | 1.7 | 1.76 | | 0.315 | 0.315 | | | | | 2.6 | 2.88 | |
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 | 20 | | 2.2 | 28290 | 26760 | 1347 | 81.4 | | 0.254 | 0.254 | | 0.28 | | RANDOM | |
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.7 | 20 | | 2.5 | | 49805 | 2507 | 93.6 | | 0.254 | 0.195 | 0.1771 | 0.211 | 0.1887 | RANDOM | |
| 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_dihedral_angle_d | 17.9 |
| x_dihedral_angle_d | 17.9 |
| x_angle_deg | 1 |
| x_angle_deg | 1 |
| x_improper_angle_d | 0.82 |
| x_improper_angle_d | 0.82 |
| x_bond_d | 0.007 |
| x_bond_d | 0.007 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 3054 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 264 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| d*TREK | data scaling |
| d*TREK | data reduction |
| LAUENORM | data reduction |
| LAUENORM | data scaling |
