2H1N
3.0 A X-ray structure of putative oligoendopeptidase F: crystals grown by vapor diffusion technique
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | Hampton research SaltRX condition #96: 0.1M Bis-Tris Propane buffer, 60% Tascimate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.87 | 68.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.987 | α = 90 |
b = 119.987 | β = 90 |
c = 249.747 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | ADJUSTABLE FOCUSING MIRRORS. K-B GEOMETRY | 2006-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | APS | 23-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 | 3 | 50 | 98.7 | 0.047 | 17.6 | 5.6 | 42052 |
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 | 3 | 3.11 | 98.3 | 0.36 | 2.1 | 5.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 3 | 20 | 41581 | 39493 | 2088 | 98.2 | 0.186 | 0.185 | 0.211 | RANDOM | 63.66 |
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] | |
0.67 | 0.34 | 0.67 | -1.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.909 |
r_dihedral_angle_3_deg | 19.001 |
r_dihedral_angle_4_deg | 17.374 |
r_dihedral_angle_1_deg | 4.871 |
r_scangle_it | 1.857 |
r_scbond_it | 1.238 |
r_angle_refined_deg | 1.047 |
r_mcangle_it | 0.733 |
r_mcbond_it | 0.537 |
r_nbtor_refined | 0.322 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9358 |
Nucleic Acid Atoms | |
Solvent Atoms | 6 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SOLVE | phasing |