3UG4
Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima arabinose complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PZ3 | PDB ENTRY 1PZ3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 1M sodium citrate, 0.1M Tris-HCl, 0.2M NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.62 | 66.07 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 100.483 | ¦Á = 90 |
b = 160.639 | ¦Â = 92.44 |
c = 154.841 | ¦Ã = 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 | CCD | ADSC QUANTUM 210r | 2010-10-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.15 | 50 | 100 | 0.108 | 20.8 | 7.7 | 266183 | 266042 | 30.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.15 | 2.23 | 100 | 0.631 | 3 | 7.6 | 26536 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1PZ3 | 2.15 | 29.99 | 266042 | 252016 | 13365 | 99.61 | 0.16924 | 0.16924 | 0.16726 | 0.20666 | RANDOM | 31.823 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.313 |
r_dihedral_angle_4_deg | 18.01 |
r_dihedral_angle_3_deg | 14.281 |
r_dihedral_angle_1_deg | 6.601 |
r_scangle_it | 4.675 |
r_scbond_it | 2.873 |
r_angle_refined_deg | 1.837 |
r_mcangle_it | 1.699 |
r_mcbond_it | 0.907 |
r_chiral_restr | 0.12 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23265 |
Nucleic Acid Atoms | |
Solvent Atoms | 1823 |
Heterogen Atoms | 398 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |