6TJQ
Crystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fluoro-beta-D-glucopyranoside
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6TJK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.112 | α = 90 |
b = 76.351 | β = 101.987 |
c = 68.16 | 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 | 2019-10-19 | 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) | 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 | 1.41 | 51.95 | 100 | 0.135 | 0.056 | 0.999 | 7.2 | 6.7 | 102363 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.41 | 7.72 | 2.388 | 0.357 | 0.4 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6TJK | 1.41 | 51.95 | 102326 | 4992 | 99.9 | 0.179 | 0.1776 | 0.2053 | 20.829 |
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] | |
0.462 | 0.748 | 1.266 | -1.876 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.684 |
r_dihedral_angle_4_deg | 20.58 |
r_dihedral_angle_1_deg | 18.896 |
r_dihedral_angle_3_deg | 13.019 |
r_lrange_it | 4.66 |
r_lrange_other | 4.399 |
r_scangle_it | 2.596 |
r_scangle_other | 2.595 |
r_scbond_it | 1.742 |
r_scbond_other | 1.741 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3923 |
Nucleic Acid Atoms | |
Solvent Atoms | 473 |
Heterogen Atoms | 177 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
MOLREP | phasing |