4OIF
3D structure of Gan42B, a GH42 beta-galactosidase from G.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4OJW | PDB ENTRY 4OJW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292 | 16-18% PEG 3350, 250 mM NaCl and 100 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.84 | α = 90 |
b = 181.35 | β = 90 |
c = 196.57 | 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 | 90 | CCD | ADSC QUANTUM 210 | mirror | 2010-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9334 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.448 | 48.86 | 96.3 | 0.113 | 0.419 | 11.7 | 5.8 | 95492 | 91957 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.45 | 2.58 | 88.6 | 0.348 | 0.419 | 4.3 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | using phases from it's GanBE323A mutant | PDB ENTRY 4OJW | 2.448 | 48.859 | 1.35 | 91878 | 91872 | 4594 | 96.23 | 0.1365 | 0.1329 | 0.2045 | 13.375 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.07 | 0.22 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.426 |
f_angle_d | 1.09 |
f_chiral_restr | 0.041 |
f_bond_d | 0.008 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16922 |
Nucleic Acid Atoms | |
Solvent Atoms | 1504 |
Heterogen Atoms | 153 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
REFMAC | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |