8IAU
Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.2 | 298 | 16.5% PEG300,50mM Na Acetate pH4.2, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM FBP, 10mM Oxalate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.3 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 73.442 | ¦Á = 88.95 |
b = 114.66 | ¦Â = 88.12 |
c = 140.705 | ¦Ã = 76.52 |
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 EIGER X 16M | Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror. | 2022-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.900 | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2 | 49.38 | 97 | 0.08 | 0.094 | 0.997 | 8.85 | 3.6 | 293893 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2 | 2.12 | 0.9179999999999999 | 1.075 | 0.598 |
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 | 2 | 49.38 | 279192 | 14695 | 96.95 | 0.20201 | 0.19966 | 0.24609 | RANDOM | 46.44 |
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] | |
1.54 | 2.05 | 0.05 | 0.35 | -0.02 | -0.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.825 |
r_dihedral_angle_4_deg | 19.688 |
r_dihedral_angle_3_deg | 17.862 |
r_long_range_B_refined | 10.202 |
r_long_range_B_other | 10.202 |
r_scangle_other | 8.233 |
r_dihedral_angle_1_deg | 7.01 |
r_mcangle_it | 6.075 |
r_mcangle_other | 6.075 |
r_scbond_it | 5.711 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 29996 |
Nucleic Acid Atoms | |
Solvent Atoms | 916 |
Heterogen Atoms | 283 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
XDS | data reduction |
MOLREP | phasing |