5A6J
GH20C, Beta-hexosaminidase from Streptococcus pneumoniae
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 |
2.22 | 44.65 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 92.84 | ¦Á = 90 |
b = 136.94 | ¦Â = 90 |
c = 202.35 | ¦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 | RIGAKU R-AXIS IV++ | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-002 |
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 | 1.94 | 50.7 | 97.4 | 0.11 | 9.2 | 3.8 | 184285 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.94 | 2.05 | 96.9 | 0.34 | 3.9 | 3.7 |
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 | 1.94 | 113.41 | 174931 | 9269 | 97.22 | 0.20853 | 0.20591 | 0.2579 | RANDOM | 19.831 |
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] | |
0.82 | -1.32 | 0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.947 |
r_dihedral_angle_4_deg | 16.946 |
r_dihedral_angle_3_deg | 12.988 |
r_dihedral_angle_1_deg | 6.228 |
r_mcangle_it | 1.594 |
r_angle_refined_deg | 1.283 |
r_scbond_it | 1.022 |
r_mcbond_it | 0.977 |
r_mcbond_other | 0.977 |
r_angle_other_deg | 0.792 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19496 |
Nucleic Acid Atoms | |
Solvent Atoms | 1619 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |