3N04
THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC 29174
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 289 | 0.1M BIS-TRIS 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.861 | α = 90 |
b = 124.97 | β = 107.74 |
c = 88.601 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | ADSC QUANTUM 315 | mirror | 2008-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97929 | APS | 19-ID |
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 | 2.02 | 44 | 99.9 | 0.149 | 14.8 | 4.6 | 93200 | 93200 |
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) | |||||||||||
2.02 | 2.07 | 99.6 | 0.644 | 2.28 | 4.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SAD | THROUGHOUT | 2.02 | 43.9 | 88427 | 88427 | 4655 | 99.13 | 0.17032 | 0.16839 | 0.20675 | RANDOM | 23.886 |
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] | |
-0.29 | 0.03 | -0.05 | 0.35 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.73 |
r_dihedral_angle_4_deg | 17.37 |
r_dihedral_angle_3_deg | 14.873 |
r_dihedral_angle_1_deg | 6.084 |
r_scangle_it | 3.247 |
r_scbond_it | 2.015 |
r_angle_refined_deg | 1.275 |
r_mcangle_it | 1.172 |
r_mcbond_it | 0.608 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10872 |
Nucleic Acid Atoms | |
Solvent Atoms | 824 |
Heterogen Atoms | 18 |
Software
Software | |
---|---|
Software Name | Purpose |
SBC-Collect | data collection |
SHELXD | phasing |
MLPHARE | phasing |
DM | model building |
ARP | model building |
WARP | model building |
HKL-3000 | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |