4HA4
Structure of beta-glycosidase from Acidilobus saccharovorans in complex with glycerol
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | Protein solution (1.5mcl): 13mg/ml Asbeta-Gly, 0.025M NaCl, 0.025M Hepes (pH 7.5). Reservoir solution (1.5mcl): 1.0M succinic acid (pH 7.0), 0.1M Hepes (pH 7.0), 1% w/v polyethylene glycol monomethyl ether 2000. The crystal was soaked in a cryoprotection solution containing 20% v/v glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.65 | 53.62 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 84.12 | α = 90 |
b = 84.12 | β = 90 |
c = 166.27 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 42 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | 2010-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | KURCHATOV SNC BEAMLINE K4.4 | 0.9815 | KURCHATOV SNC | K4.4 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.37 | 19.827 | 98.8 | 0.063 | 17.2 | 124046 | 20.1 |
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 | 1.37 | 1.45 | 96.5 | 0.81 | 2.1 | 18722 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.37 | 19.827 | 117803 | 6243 | 98.83 | 0.13213 | 0.13049 | 0.1296 | 0.16333 | 0.1621 | RANDOM | 15.182 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-0.27 | -0.27 | 0.55 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.875 |
r_dihedral_angle_4_deg | 15.576 |
r_dihedral_angle_3_deg | 12.343 |
r_sphericity_free | 7.943 |
r_dihedral_angle_1_deg | 6.226 |
r_scangle_it | 3.974 |
r_sphericity_bonded | 3.704 |
r_scbond_it | 2.945 |
r_mcangle_it | 2.075 |
r_angle_refined_deg | 1.559 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3909 |
Nucleic Acid Atoms | |
Solvent Atoms | 543 |
Heterogen Atoms | 72 |
Software
Software | |
---|---|
Software Name | Purpose |
AUTOMAR | data collection |
BALBES | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |