6YTR
Structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol aziridine inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NT0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 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 |
3.07 | 59.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.155 | α = 90 |
b = 156.779 | β = 102.116 |
c = 68.23 | 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 X 16M | 2021-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9762 | Diamond | I02 |
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 | 1.7 | 66.799 | 99.9 | 0.159 | 0.064 | 0.994 | 6.3 | 6.6 | 119361 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 1.73 | 99.7 | 1.83 | 1.07 | 0.547 | 1 |
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 | 2NT0 | 1.7 | 66.799 | 119361 | 5927 | 99.883 | 0.161 | 0.1592 | 0.2026 | 24.919 |
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] | |
0.659 | 0.144 | 0.625 | -1.233 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_other_1_deg | 48.62 |
r_dihedral_angle_2_deg | 33.948 |
r_dihedral_angle_4_deg | 19.2 |
r_dihedral_angle_3_deg | 13.438 |
r_dihedral_angle_1_deg | 7.497 |
r_lrange_it | 5.163 |
r_lrange_other | 5.162 |
r_scangle_it | 3.628 |
r_scangle_other | 3.628 |
r_scbond_it | 2.57 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7833 |
Nucleic Acid Atoms | |
Solvent Atoms | 877 |
Heterogen Atoms | 360 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
MOLREP | phasing |