4KWB
Structure of signal peptide peptidase A with C-termini bound in the active sites: insights into specificity, self-processing and regulation
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 298.15 | 100mM TRIS, 23% TERT-BUTANOL UNDER PARAFFIN OIL, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K, pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.797 | α = 90 |
b = 130.979 | β = 90 |
c = 207.099 | 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 | RAYONIX MX-300 | VERTICAL COLLIMATING MIRROR | 2011-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97949 | CLSI | 08ID-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.39 | 50 | 99.2 | 0.06 | 50.3 | 6.8 | 93912 | 93168 | 2 | -3 | 51 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.39 | 2.49 | 97.5 | 0.302 | 6.7 | 6.3 | 9085 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3BFO | 2.39 | 50 | 93310 | 88919 | 4708 | 98.7 | 0.285 | 0.208 | 0.206 | 0.24 | RANDOM | 50.9 |
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] | |
-0.36 | 1.59 | -1.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.134 |
r_dihedral_angle_3_deg | 15.578 |
r_dihedral_angle_4_deg | 14.969 |
r_dihedral_angle_1_deg | 5.257 |
r_scangle_it | 2.576 |
r_scbond_it | 1.524 |
r_angle_refined_deg | 1.061 |
r_mcangle_it | 0.898 |
r_mcbond_it | 0.451 |
r_chiral_restr | 0.069 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14103 |
Nucleic Acid Atoms | |
Solvent Atoms | 221 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MxDC | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |