3B2Y
CRYSTAL STRUCTURE OF a putative metallopeptidase (SDEN_2526) FROM SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.07 | 277 | NANODROP, 20.4% PEG 6000, 0.1M MES pH 6.07, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 38.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.715 | α = 90 |
b = 127.577 | β = 116.28 |
c = 49.303 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 315 | KOHZU, Double crystal Si(111) | 2007-09-14 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.9794, 1.0000, 0.9797 | ALS | 8.2.1 |
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 | 1.74 | 28.82 | 94.7 | 0.047 | 0.047 | 7.6 | 1.9 | 46761 | 28.085 |
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 | 1.74 | 1.79 | 95.4 | 0.38 | 0.38 | 2 | 1.7 | 3475 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.74 | 28.82 | 46725 | 2353 | 94.32 | 0.176 | 0.175 | 0.215 | RANDOM | 28.462 |
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] | |
0.82 | 1.49 | -1.84 | 2.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.16 |
r_dihedral_angle_4_deg | 15.357 |
r_dihedral_angle_3_deg | 13.771 |
r_scangle_it | 8.064 |
r_dihedral_angle_1_deg | 6.263 |
r_scbond_it | 6.017 |
r_mcangle_it | 3.614 |
r_mcbond_it | 2.651 |
r_angle_refined_deg | 1.669 |
r_angle_other_deg | 1.143 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4016 |
Nucleic Acid Atoms | |
Solvent Atoms | 230 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
ADSC | data collection |
MOSFLM | data reduction |
SHARP | phasing |