8Q1F
D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with native beta-glucose 1,6-bisphosphate intermediate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WF9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 290 | 0.6 mM bPGM-D10N,P146A 50 mM MgCl2 10 mM bG16BP 28% PEG 4000 100 mM sodium acetate 100 mM tris |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.023 | α = 90 |
b = 79.663 | β = 97.614 |
c = 79.848 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 EIGER2 XE 16M | 2023-02-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9801 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.01 | 39.83 | 80.3 | 0.038 | 0.016 | 0.999 | 26 | 6.3 | 166355 | 7.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.01 | 1.03 | 0.494 | 0.386 | 0.743 | 0.8 | 1.6 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.01 | 39.83 | 166313 | 8222 | 80.296 | 0.116 | 0.1152 | 0.1348 | 14.316 |
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] | |
-0.047 | 0.046 | 0.618 | -0.564 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_rigid_bond_restr | 28.835 |
r_dihedral_angle_6_deg | 14.984 |
r_dihedral_angle_3_deg | 12.209 |
r_dihedral_angle_1_deg | 5.525 |
r_dihedral_angle_2_deg | 4.599 |
r_angle_refined_deg | 1.486 |
r_angle_other_deg | 0.519 |
r_symmetry_nbd_refined | 0.246 |
r_nbd_refined | 0.235 |
r_nbd_other | 0.198 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3412 |
Nucleic Acid Atoms | |
Solvent Atoms | 485 |
Heterogen Atoms | 67 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |