8Q57
Crystal structure of class II SFP aldolase from Yersinia aldovae (YaSqiA-Zn-SO4) with bound sulfate ions
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5UCK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | Protein at 16 mg mL-1 in 50 mM NaPi, 300 mM NaCl buffer pH 7.4, using a drop containing 0.6 uL protein and 0.5 uL mother liquor, the latter comprising 1.5 M ammonium sulfate, 0.1 M NaCl, 0.1 M BIS-TRIS pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.08 | 60.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.734 | α = 90 |
b = 87.525 | β = 107.73 |
c = 104.312 | γ = 90 |
Symmetry | |
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Space Group | I 1 2 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 PILATUS3 2M | 2020-01-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.7 | 61.5 | 100 | 0.073 | 0.079 | 0.03 | 0.999 | 12.9 | 7.1 | 85319 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.7 | 1.73 | 99.9 | 1.181 | 1.276 | 0.481 | 0.752 | 6.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.7 | 61.01 | 81063 | 4241 | 99.95 | 0.18579 | 0.18477 | 0.20522 | RANDOM | 28.012 |
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] | |
-1.35 | 0.06 | -1.26 | 2.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 13.32 |
r_dihedral_angle_2_deg | 9.819 |
r_long_range_B_refined | 6.851 |
r_long_range_B_other | 6.85 |
r_dihedral_angle_1_deg | 5.73 |
r_scangle_other | 5.652 |
r_scbond_it | 3.892 |
r_scbond_other | 3.891 |
r_mcangle_it | 3.619 |
r_mcangle_other | 3.618 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4181 |
Nucleic Acid Atoms | |
Solvent Atoms | 271 |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
xia2 | data reduction |
MOLREP | phasing |