3KBV
Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | batch | 7.7 | 290 | 40mg/ml protein, 5mM NiCl2, 30% (v/v) ammonium sulfate (sat.), pH 7.7, batch, temperature 290K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.78 | 55.75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 93.99 | α = 90 |
| b = 99.47 | β = 90 |
| c = 102.96 | 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 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2008-10-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | 1.54 | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.8 | 20 | 92 | 44836 | 41073 | 4 | 2 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 1.8 | 1.88 | 95 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | AB INITIO | FREE R | 1.8 | 20 | 44836 | 2235 | 99.7 | 0.1836 | 0.1811 | 0.2231 | 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 3275.5 | ||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_similar_adp_cmpnt | 0.074 |
| s_non_zero_chiral_vol | 0.052 |
| s_zero_chiral_vol | 0.042 |
| s_angle_d | 0.023 |
| s_from_restr_planes | 0.0224 |
| s_anti_bump_dis_restr | 0.014 |
| s_bond_d | 0.008 |
| s_similar_dist | |
| s_rigid_bond_adp_cmpnt | |
| s_approx_iso_adps | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3053 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 224 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrystalClear | data collection |
| SHELX | model building |
| SHELXL-97 | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
| SHELX | phasing |
