4PQ9
Crystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 289 | MCSG1(a7): 25% PEG3350, Bis-Tris:HCl, pH=5.5, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.73 | 28.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.12 | α = 109.45 |
b = 46.84 | β = 95.63 |
c = 51.84 | γ = 99.79 |
Symmetry | |
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Space Group | P 1 |
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 | MARMOSAIC 225 mm CCD | Beryllium Lenses | 2014-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97857 | APS | 21-ID-F |
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 | 1.2 | 50 | 94.3 | 0.032 | 26.2 | 3.9 | 121825 | 114838 | -3 | 12.164 |
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 | 1.2 | 1.23 | 91.3 | 0.131 | 9.54 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 3rq0 | 1.2 | 48.2 | 120457 | 114838 | 5619 | 94.38 | 0.1189 | 0.1176 | 0.1435 | RANDOM | 10.217 |
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] | |
0.32 | 0.08 | 0.19 | -0.24 | -0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.729 |
r_sphericity_free | 29.896 |
r_dihedral_angle_4_deg | 16.585 |
r_dihedral_angle_3_deg | 11.796 |
r_sphericity_bonded | 7.61 |
r_dihedral_angle_1_deg | 7.122 |
r_rigid_bond_restr | 1.655 |
r_mcangle_it | 1.613 |
r_angle_refined_deg | 1.57 |
r_mcbond_it | 1.222 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3696 |
Nucleic Acid Atoms | |
Solvent Atoms | 558 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
BALBES | phasing |