3HKX
Crystal structure analysis of an amidase from Nesterenkonia sp.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1F89 | PDB entry 1F89 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 0.1M Sodium acetate trihydrate and 2M ammonium sulphate, pH 4.6, vapor diffusion, hanging drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.999 | α = 90 |
b = 115.639 | β = 90 |
c = 65.321 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 123 | CCD | MARMOSAIC 225 mm CCD | J. Synchrotron Rad. (1999). 6, 822-833 Development of instrumentation and methods for MAD and structural genomics at the SRS, ESRF, CHESS and Elettra facilities A. Cassetta, A. M. Deacon, S. E. Ealick, J. R. Helliwell and A. W. Thompson | 2009-01-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.9778 | ESRF | BM14 |
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 | 1.66 | 63.511 | 99.9 | 0.046 | 15.6 | 7.03 | 34246 | 34232 | 3 | 3 |
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 | 1.66 | 1.72 | 98.9 | 0.36 | 4.2 | 6.92 |
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 1F89 | 1.66 | 63.5 | 32495 | 1727 | 99.58 | 0.18713 | 0.18566 | 0.21433 | RANDOM | 25.576 |
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] | |
0.73 | 0.38 | -1.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.856 |
r_dihedral_angle_4_deg | 14.311 |
r_dihedral_angle_3_deg | 14.035 |
r_dihedral_angle_1_deg | 6.565 |
r_scangle_it | 6.238 |
r_scbond_it | 3.965 |
r_mcangle_it | 2.704 |
r_mcbond_it | 1.76 |
r_angle_refined_deg | 1.674 |
r_chiral_restr | 0.156 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1970 |
Nucleic Acid Atoms | |
Solvent Atoms | 194 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MxCuBE | data collection |
d*TREK | data reduction |
d*TREK | data scaling |