3KBW
Room temperature X-ray mixed-metal structure of D-Xylose Isomerase in complex with Ni(2+) and Mg(2+) co-factors
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | batch | 7.7 | 290 | 40mg/ml protein, 2mM NiCl2, 2mM MgCl2, 30% (v/v) ammonium sulfate (sat.), pH 7.7, batch, temperature 290K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.78 | 55.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.972 | α = 90 |
b = 99.701 | β = 90 |
c = 102.855 | γ = 90 |
Symmetry | |
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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++ | 2008-08-26 | 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 | 1.6 | 10 | 80 | 62867 | 50014 | 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 | 1.6 | 1.65 | 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 | 1.6 | 10 | 62867 | 3131 | 98.9 | 0.1216 | 0.1192 | 0.1665 | 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 |
3 | 3338 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.114 |
s_non_zero_chiral_vol | 0.063 |
s_similar_adp_cmpnt | 0.061 |
s_zero_chiral_vol | 0.047 |
s_angle_d | 0.029 |
s_from_restr_planes | 0.0232 |
s_anti_bump_dis_restr | 0.015 |
s_bond_d | 0.012 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3053 |
Nucleic Acid Atoms | |
Solvent Atoms | 312 |
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 |