4WVG
Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB).
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 296 | 12 % PEG 8000, 20 % ethylene glycol, 0.2 M amino acids mix (0.2 M sodium-L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine, 0.2 M DL-serine), 100 mM Tris.Cl pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.683 | α = 90 |
b = 63.565 | β = 92.59 |
c = 79.892 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 210r | 2013-03-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 2.05 | 19.44 | 99.8 | 0.211 | 0.082 | 0.994 | 10.1 | 7.6 | 36318 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.05 | 2.11 | 99.8 | 1.577 | 0.608 | 0.528 | 1.4 | 7.6 | 2779 |
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 | 1ANF | 2.05 | 19.44 | 34468 | 1839 | 99.72 | 0.1921 | 0.1896 | 0.242 | RANDOM | 29.325 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.72 | -0.32 | -0.51 | 1.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.687 |
r_dihedral_angle_3_deg | 12.969 |
r_dihedral_angle_4_deg | 8.241 |
r_dihedral_angle_1_deg | 5.331 |
r_mcangle_it | 2.211 |
r_mcbond_it | 1.296 |
r_mcbond_other | 1.296 |
r_angle_refined_deg | 1.16 |
r_angle_other_deg | 0.717 |
r_chiral_restr | 0.066 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3977 |
Nucleic Acid Atoms | |
Solvent Atoms | 356 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |