6ZA2
Crystal structure of dimeric latent PorU from Porphyromonas gingivalis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | The best crystals of full-length native and selenomethionine-derivatized PorU were obtained at 20 degrees in drops with 1 microL of protein solution (at 5-10 mg per mL in 20 mM Tris-HCl, 150 mM NaCl, pH 7.5) and 1 microL of reservoir solution (100 mM HEPES, 200 mM calcium chloride, 28-32 per cent v/v PEG600, pH 7.5). Crystals were cryoprotected by rapid passage through drops containing increasing amounts of glycerol (5-to-20 per cent v/v). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.65 | 66.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 171.7 | α = 90 |
b = 171.7 | β = 90 |
c = 440.4 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 | 110 | PIXEL | DECTRIS PILATUS3 6M | 2017-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.9817 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 3.35 | 88.48 | 100 | 0.152 | 0.154 | 1 | 22.71 | 38.5 | 56055 | 107 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.35 | 3.55 | 100 | 1.899 | 1.923 | 0.844 | 3.12 | 39.626 |
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 | 3.35 | 88.48 | 56054 | 836 | 100 | 0.203 | 0.202 | 0.243 | RANDOM | 140.3 |
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] | |
-7.7643 | -7.7643 | 15.5285 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_omega_torsion | 3.65 |
t_other_torsion | 3.29 |
t_angle_deg | 1.15 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16378 |
Nucleic Acid Atoms | |
Solvent Atoms | 4 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXDE | phasing |