6RS1
Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Lithium Sulfate, 0.1 M Bis-Tris pH 6.2 and 25% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.567 | α = 79.95 |
b = 67.636 | β = 73.13 |
c = 88.908 | γ = 65.58 |
Symmetry | |
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Space Group | P 1 |
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 | PIXEL | DECTRIS PILATUS 6M-F | 2018-06-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.072 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.9 | 48.37 | 83.45 | 0.178 | 0.2 | 0.09 | 0.992 | 7.04 | 4.9 | 88957 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 2.04 | 1.194 | 1.34 | 0.6 | 0.623 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5KY6 | 1.9 | 48.37 | 73398 | 3860 | 71.13 | 0.21631 | 0.21435 | 0.25381 | RANDOM | 20.153 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.08 | -0.21 | 0.03 | 0.11 | 0.04 | -0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.96 |
r_dihedral_angle_4_deg | 24.257 |
r_dihedral_angle_3_deg | 17.854 |
r_dihedral_angle_1_deg | 6.603 |
r_long_range_B_refined | 3.604 |
r_long_range_B_other | 3.462 |
r_angle_refined_deg | 1.566 |
r_mcangle_it | 1.296 |
r_mcangle_other | 1.296 |
r_angle_other_deg | 0.98 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10156 |
Nucleic Acid Atoms | |
Solvent Atoms | 614 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |