6BXG
1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.3 | 292 | Protein: 9.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: PACT (E3) 0.2M Sodium iodide, 20% (w/v) PEG 3350.. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 33.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.579 | α = 90 |
b = 35.579 | β = 90 |
c = 118.394 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 300 mm CCD | C(111) | 2017-08-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.45 | 30 | 99.9 | 0.054 | 0.054 | 0.058 | 0.021 | 51.2 | 7.4 | 15127 | -3 | 19.6 |
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) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.45 | 1.48 | 100 | 0.759 | 0.759 | 0.817 | 0.3 | 0.893 | 2.9 | 7.3 |
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 | 1.45 | 29.82 | 14288 | 708 | 99.94 | 0.1346 | 0.1324 | 0.17758 | RANDOM | 25.91 |
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] | |
-0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 28.8 |
r_dihedral_angle_2_deg | 28.59 |
r_dihedral_angle_4_deg | 19.569 |
r_sphericity_bonded | 16.515 |
r_rigid_bond_restr | 11.997 |
r_dihedral_angle_3_deg | 9.647 |
r_long_range_B_refined | 3.902 |
r_long_range_B_other | 3.779 |
r_dihedral_angle_1_deg | 3.325 |
r_scangle_other | 2.595 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 754 |
Nucleic Acid Atoms | |
Solvent Atoms | 84 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |