6H8W
Beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with aluminium tetrafluoride to 1.9 A.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 291 | Crystals initially grown as open beta-phosphoglucomutase crystals, using 24-32% PEG 4000, 200mM sodium acetate, 50 mM TRIS buffer pH 7.5. Crystals were cryoprotected in their original mother liquor with the addition of 25% ethylene glycol, 5 mM aluminium chloride and 20 mM sodium fluoride. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.44 | α = 90 |
b = 53.71 | β = 90 |
c = 80.88 | 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 | PIXEL | DECTRIS PILATUS 6M-F | 2015-11-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97949 | 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 | 1.98 | 40.44 | 99.8 | 0.116 | 0.156 | 0.075 | 0.992 | 9.5 | 4.3 | 71414 | 19779 |
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 | 1.98 | 2.03 | 99.9 | 0.738 | 0.969 | 0.459 | 0.576 | 4.3 |
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 | 2WHE | 1.98 | 40.44 | 15929 | 807 | 99.79 | 0.20666 | 0.20457 | 0.24806 | RANDOM | 24.376 |
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] | |
1.12 | -1.08 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 43.341 |
r_dihedral_angle_4_deg | 21.855 |
r_dihedral_angle_3_deg | 14.096 |
r_dihedral_angle_1_deg | 5.848 |
r_long_range_B_refined | 4.49 |
r_long_range_B_other | 4.45 |
r_scangle_other | 3.174 |
r_mcangle_it | 2.475 |
r_mcangle_other | 2.474 |
r_scbond_other | 2.045 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1689 |
Nucleic Acid Atoms | |
Solvent Atoms | 136 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
MOLREP | phasing |
xia2 | data reduction |