1KN9
CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B12 | PDB ENTRY 1B12 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.4 | 295 | ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.441 | α = 90 |
b = 112.441 | β = 90 |
c = 198.675 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | 100 | IMAGE PLATE | MARRESEARCH | mirrors | 2000-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.08000 | SSRL | BL7-1 |
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 | 2.4 | 50 | 98.8 | 0.041 | 25.4 | 49984 | 49984 | 2 | 2 | 39.6 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.4 | 2.49 | 100 | 0.296 | 5.8 |
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 | PDB ENTRY 1B12 | 2.4 | 40.05 | 49984 | 49920 | 2491 | 98.7 | 0.239 | 0.239 | 0.239 | 0.278 | RANDOM | 45.6 |
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] | |
2.07 | 2.07 | -4.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 26.7 |
c_scangle_it | 3.03 |
c_mcangle_it | 2.71 |
c_scbond_it | 2.03 |
c_mcbond_it | 1.71 |
c_angle_deg | 1.5 |
c_improper_angle_d | 0.82 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6898 |
Nucleic Acid Atoms | |
Solvent Atoms | 256 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |