3KPF
X-ray structure of the mutant Lys300Met of polyamine oxidase from Zea mays
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B37 | PDB ENTRY 1B37 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.6 | 293 | 50% SATURATED AMMONIUM SULFATE SOLUTION, 0.1M SODIUM ACETATE pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.82 | 74.47 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 138.606 | ¦Á = 90 |
b = 138.606 | ¦Â = 90 |
c = 189.471 | ¦Ã = 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 | CCD | MARMOSAIC 225 mm CCD | 2009-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | BESSY | 14.1 |
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 | 2.9 | 50 | 96.9 | 0.133 | 10.4 | 4 | 45830 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.9 | 2.97 | 98.1 | 0.454 | 3 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 1B37 | 2.9 | 50 | -3 | 43422 | 2312 | 96.9 | 0.188 | 0.186 | 0.223 | RANDOM | 24.19 |
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] | |
1.29 | 0.64 | 1.29 | -1.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.933 |
r_dihedral_angle_3_deg | 15.897 |
r_dihedral_angle_4_deg | 14.715 |
r_dihedral_angle_1_deg | 6.651 |
r_scangle_it | 1.933 |
r_angle_refined_deg | 1.22 |
r_scbond_it | 1.1 |
r_mcangle_it | 0.785 |
r_mcbond_it | 0.41 |
r_chiral_restr | 0.082 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7473 |
Nucleic Acid Atoms | |
Solvent Atoms | 171 |
Heterogen Atoms | 162 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |