4WVI
Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep2).
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4WVG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 290 | 12 % PEG 8000, 20 % ethylene glycol, 100 mM sodium acetate pH 5.3 - 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.989 | α = 90 |
b = 80.232 | β = 90 |
c = 119.879 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 315r | 2014-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
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 | 1.9 | 19.78 | 99.9 | 0.19 | 0.064 | 0.997 | 11.1 | 9.5 | 49376 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 1.94 | 100 | 2.077 | 0.698 | 0.514 | 1.5 | 9.5 | 3283 |
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 | 4WVG | 1.9 | 19.78 | 46809 | 2503 | 99.83 | 0.1895 | 0.1879 | 0.2194 | RANDOM | 24.36 |
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] | |
0.37 | -0.6 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.15 |
r_dihedral_angle_4_deg | 13.638 |
r_dihedral_angle_3_deg | 12.378 |
r_dihedral_angle_1_deg | 5.633 |
r_mcangle_it | 2.074 |
r_mcbond_it | 1.275 |
r_mcbond_other | 1.27 |
r_angle_refined_deg | 1.215 |
r_angle_other_deg | 0.741 |
r_chiral_restr | 0.072 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4075 |
Nucleic Acid Atoms | |
Solvent Atoms | 371 |
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 |