3GIU
1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 295 | protein solution: 0.3M NaCl, 10mM Hepes pH 7.5; Screen solution: 20% PEG3350, Sodium Acetate 0.1M pH 4.5; Cryo solution: 7% Glycerol, 7% Ethilene Glycol, 7% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.79 | α = 90 |
b = 81 | β = 90 |
c = 119.91 | 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 | MARMOSAIC 300 mm CCD | beryllium lenses | 2008-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.72900 | APS | 21-ID-D |
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 | 1.25 | 24.55 | 99 | 0.047 | 19.1 | 5.6 | 114545 | 114545 | -3 | 10.7 |
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) | |||||||||||
1 | 1.25 | 1.32 | 95.1 | 0.404 | 3.6 | 4.5 | 15769 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.25 | 24.55 | 108305 | 108305 | 5691 | 98.31 | 0.11775 | 0.11775 | 0.11616 | 0.14782 | RANDOM | 9.118 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.66 | 0.95 | -0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.749 |
r_sphericity_free | 17.89 |
r_dihedral_angle_4_deg | 11.238 |
r_dihedral_angle_3_deg | 10.161 |
r_scangle_it | 5.697 |
r_dihedral_angle_1_deg | 5.398 |
r_sphericity_bonded | 4.952 |
r_scbond_it | 3.987 |
r_mcangle_it | 2.713 |
r_mcbond_it | 1.886 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3277 |
Nucleic Acid Atoms | |
Solvent Atoms | 619 |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
SHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |