5A6K
GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2EPN | PDB ENTRY 2EPN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 10.2 | 12% (W/V) PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.05 M CAPS, PH 10.2, 1% GLYCEROL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.11 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 95.69 | ¦Á = 90 |
b = 99.42 | ¦Â = 90 |
c = 133.17 | ¦Ã = 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 | 291 | CCD | MARMOSAIC 225 mm CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | CLSI | 08ID-1 |
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 | 95.69 | 92.9 | 0.12 | 11.1 | 6.4 | 69114 | 2 |
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 | 2.21 | 84.5 | 0.24 | 6 | 5.9 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2EPN | 2.1 | 79.67 | 65678 | 3339 | 92.46 | 0.17501 | 0.17255 | 0.22393 | RANDOM | 14.154 |
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] | |
2.13 | -2.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.234 |
r_dihedral_angle_4_deg | 17.11 |
r_dihedral_angle_3_deg | 12.346 |
r_dihedral_angle_1_deg | 6.082 |
r_angle_refined_deg | 1.329 |
r_mcangle_it | 1.182 |
r_scbond_it | 0.965 |
r_angle_other_deg | 0.814 |
r_mcbond_it | 0.701 |
r_mcbond_other | 0.701 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9970 |
Nucleic Acid Atoms | |
Solvent Atoms | 1096 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |