3KI9
Crystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the Mn2+ bound form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KHX | PDB ENTRY 3KHX, independent domains |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Microbatch method under oil | 6.8 | 293 | 0.2M Megnesium Acetate tetrahydrate, 0.1M Sodium Cacodylate pH 6.8, 22.0% Polyethylene glycol 8000, Microbatch method under oil, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.98 | 58.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 158.15 | α = 90 |
b = 158.15 | β = 90 |
c = 158.15 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | RIGAKU | 2009-07-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | OTHER | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.9 | 50 | 100 | 0.108 | 0.115 | 14.2 | 7.9 | 14758 | 2 | 2 | 69.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.9 | 3.06 | 100 | 0.563 | 0.604 | 3.6 | 7.8 | 2141 |
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 | PDB ENTRY 3KHX, independent domains | 2.9 | 28.88 | 13998 | 745 | 99.99 | 0.20492 | 0.20212 | 0.2626 | RANDOM | 42.555 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.888 |
r_dihedral_angle_4_deg | 20.69 |
r_dihedral_angle_3_deg | 15.345 |
r_dihedral_angle_1_deg | 4.845 |
r_scangle_it | 1.232 |
r_angle_refined_deg | 0.937 |
r_scbond_it | 0.695 |
r_mcangle_it | 0.577 |
r_mcbond_it | 0.304 |
r_chiral_restr | 0.065 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3662 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |