2OKX
Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 13.5%(W/V) PEG 8000, 0.08M sodium cacodylate, 0.16M calcium acetate, 20%(V/V) glycerol, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 57.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.744 | α = 90 |
b = 119.985 | β = 90 |
c = 207.352 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | RIGAKU JUPITER 210 | MIRRORS | 2006-03-20 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | RIGAKU JUPITER 210 | MIRRORS | 2005-03-15 | M | SINGLE WAVELENGTH | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.00 | SPring-8 | BL38B1 |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 0.97916 | SPring-8 | BL38B1 |
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 | 1.9 | 49.4 | 98.8 | 0.066 | 11.2 | 5.3 | 188971 | -3 | 17.4 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 1.97 | 91 | 0.407 | 2.1 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | SAD | THROUGHOUT | SAD MODEL | 1.9 | 15 | 188458 | 18716 | 98.5 | 0.182 | 0.182 | 0.214 | RANDOM | 30.1 |
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] | |
7.87 | -3.69 | -4.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.1 |
c_scangle_it | 2.5 |
c_scbond_it | 1.76 |
c_mcangle_it | 1.71 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.15 |
c_improper_angle_d | 0.76 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14954 |
Nucleic Acid Atoms | |
Solvent Atoms | 1755 |
Heterogen Atoms | 262 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |
RESOLVE | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
CNS | phasing |