5LVX
Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4.5 | 293 | 20 %w/v PEG 3350 0.2 M (NH4)2SO4 0.1 M Na Acet pH=4.50 0.50 %w/v LDAO |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.91 | α = 90 |
b = 132.281 | β = 95.26 |
c = 103.085 | 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 PILATUS3 6M | 2015-09-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.999 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.2 | 102.65 | 97.5 | 0.061 | 2.2 | 125199 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.45 | 98.3 | 0.431 | 2.2 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | OTHER | THROUGHOUT | 2.2 | 102.65 | 123670 | 1529 | 97.56 | 0.18907 | 0.18881 | 0.21014 | RANDOM | 39.374 |
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] | |
-0.39 | 0.41 | -1.5 | 1.78 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.328 |
r_dihedral_angle_4_deg | 16.472 |
r_dihedral_angle_3_deg | 12.783 |
r_long_range_B_refined | 8.683 |
r_long_range_B_other | 8.619 |
r_scangle_other | 7.926 |
r_dihedral_angle_1_deg | 6.47 |
r_scbond_it | 6.362 |
r_scbond_other | 6.191 |
r_mcangle_it | 6.172 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15714 |
Nucleic Acid Atoms | |
Solvent Atoms | 681 |
Heterogen Atoms | 518 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |