Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4c
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5NN3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 1.9 M AMMONIUM SULPHATE, 0.1 M HEPES, REMARK 280 2% V/V PEG400, PH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.4 | 63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.372 | α = 90 |
b = 102.298 | β = 90 |
c = 128.155 | 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 EIGER X 16M | 2018-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.978570 | SOLEIL | PROXIMA 1 |
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 | 1.8 | 48.23 | 99.9 | 0.091 | 0.099 | 0.039 | 0.998 | 11.3 | 6.6 | 117618 | 26.2 |
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 | 1.8 | 1.83 | 1.378 | 1.492 | 0.569 | 0.536 | 1.3 | 6.7 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R-VALUE | 1.8 | 48.23 | 111674 | 5855 | 99.84 | 0.16192 | 0.16038 | 0.1711 | 0.19168 | 0.2025 | Taken over from parent data set | 30.96 |
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] | |
0.98 | -0.22 | -0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.114 |
r_dihedral_angle_4_deg | 16.356 |
r_dihedral_angle_3_deg | 12.104 |
r_long_range_B_other | 9.432 |
r_long_range_B_refined | 9.412 |
r_scangle_other | 9.337 |
r_scbond_it | 7.434 |
r_scbond_other | 7.433 |
r_dihedral_angle_1_deg | 7.127 |
r_mcangle_it | 4.502 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6631 |
Nucleic Acid Atoms | |
Solvent Atoms | 475 |
Heterogen Atoms | 293 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
REFMAC | phasing |