4XHC
rhamnosidase from Klebsiella oxytoca with rhamnose bound
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 10% (w/v) PEG 3350, 200 mM MgSO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.68 | 73.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 148.43 | α = 90 |
b = 148.43 | β = 90 |
c = 202.16 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | PIXEL | DECTRIS PILATUS 6M | 2012-07-07 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M | 2012-12-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.068 | Diamond | I24 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.920 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 2.7 | 63.07 | 98.5 | 0.125 | 0.061 | 0.995 | 9.7 | 4.9 | 61251 | 41.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.7 | 2.77 | 99 | 1.077 | 0.522 | 0.625 | 1.4 | 5 | 4450 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.7 | 63.07 | 58166 | 3084 | 97.97 | 0.1833 | 0.1823 | 0.2022 | RANDOM | 56.8 |
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] | |
-1.16 | -1.16 | 2.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.095 |
r_dihedral_angle_4_deg | 18.189 |
r_dihedral_angle_3_deg | 13.812 |
r_dihedral_angle_1_deg | 5.518 |
r_mcangle_it | 1.985 |
r_mcbond_it | 1.225 |
r_mcbond_other | 1.225 |
r_angle_refined_deg | 1.134 |
r_angle_other_deg | 0.811 |
r_chiral_restr | 0.064 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8246 |
Nucleic Acid Atoms | |
Solvent Atoms | 45 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
SHELX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Aimless | data scaling |