1LK5
Structure of the D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 294 | 0.1M HEPES-Na buffer, 0.8M Na-phosphate, 0.8M K-phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.548 | α = 90 |
b = 114.932 | β = 90 |
c = 119.017 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | M | SINGLE WAVELENGTH | |||||||
2 | 1 | IMAGE PLATE | MARRESEARCH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.9326 | ESRF | ID14-2 |
2 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 1.75 | 15 | 98.89 | 101977 | 100845 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.75 | 1.83 | 97.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MIR | THROUGHOUT | 1.75 | 15 | 101977 | 100845 | 5101 | 0.192 | 0.192 | 0.191 | 0.2 | 0.215 | 0.22 | RANDOM |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_angle_refined_deg | 1.314 |
r_bond_refined_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7064 |
Nucleic Acid Atoms | |
Solvent Atoms | 644 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALA | data scaling |
MLPHARE | phasing |
CNS | refinement |
CCP4 | data scaling |