6ORI
Enterococcal surface protein, partial N-terminal region
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | Crystallization condition: protein: 7.5 mg/mL in 10 mM Tris and 10 mM NaCl Mother liquid: 0.2 M ammonium acetate, pH 7.0, 16% PEG3350, 1 uL mother liquid + 1 uL protein The crystal was soaked in 8.625%(w/v) sodium acrylate, 2.5%(w/v) acrylamide and 0.2%(w/v) bis-acrylamide in mother liquid (0.2 M ammonium acetate, pH 7.0, 16% PEG 3350). after soaking for over 48 hours, the crystal was transferred to 1% APS and 1% TEMED in mother liquid (0.2 M ammonium acetate, pH 7.0, 16% PEG 3350). after 10 min, calcium chloride was added to the crystal with a final concentration of 100 mM. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 37.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.85 | α = 107.36 |
b = 49.96 | β = 111.42 |
c = 51.2399 | γ = 90.43 |
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 | PIXEL | DECTRIS PILATUS 6M | 2018-05-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 0.9801 | ALS | 5.0.2 |
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 | 1.4 | 47.27 | 85.4095 | 0.066 | 15.1 | 3.17 | 58580 | 8.90025571117 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.4 | 1.42 | 78.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | Crystals with selenomethionine previously determined by our lab but unpublished | 1.4 | 47.27 | 1.98 | 58577 | 2932 | 85.4 | 0.1531 | 0.152 | 0.1738 | 13.1 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.8461448209 |
f_angle_d | 1.24042777997 |
f_chiral_restr | 0.0763462994011 |
f_bond_d | 0.0092861163331 |
f_plane_restr | 0.0056447185071 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3025 |
Nucleic Acid Atoms | |
Solvent Atoms | 433 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
ELVES | data processing |
MOSFLM | data reduction |
Aimless | data scaling |
PHENIX | model building |
MOLREP | phasing |