7BYS
Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 2.1 M ammonium sulfate, 0.1 M citrate buffer pH 5.5. |
2 | VAPOR DIFFUSION | 5.5 | 293 | 16% (w/v) polyethylene glycol (PEG) 10000 95 mM ammonium sulfate 95 mM bis-tris 4.8% (v/v) glycerol |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.05 | 40.03 |
2.47 | 50.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.47 | α = 72.03 |
b = 66.262 | β = 84.68 |
c = 74.021 | γ = 82.15 |
Symmetry | |
---|---|
Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 95 | CCD | ADSC QUANTUM 315 | 2008-02-11 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 95 | CCD | ADSC QUANTUM 4r | 2008-11-26 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 0.90646 | Photon Factory | BL-5A |
2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6A | 0.97882,0.97950,0.98300,0.96400 | Photon Factory | BL-6A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.4 | 50 | 95.6 | 0.054 | 22.4 | 1.9 | 136692 |
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 | 1.4 | 1.45 | 89 | 0.37 | 2.8 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MAD | FREE R-VALUE | 1.4 | 8 | 1.96 | 136655 | 6862 | 95.46 | 0.1562 | 0.1547 | 0.1856 | Random selection | 17.1719 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6436 |
Nucleic Acid Atoms | |
Solvent Atoms | 1242 |
Heterogen Atoms | 109 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
REFMAC | refinement |
Coot | model building |
MOLREP | phasing |
ARP/wARP | model building |
SOLVE | phasing |
RESOLVE | phasing |
DENZO | data reduction |
SCALEPACK | data scaling |