3KJM
Leu492Ala mutant of Maize cytokinin oxidase/dehydrogenase complexed with phenylurea inhibitor CPPU
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QPM | PDB ENTRY 2QPM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 31% (w/v) PEG 1500, 0.5% (w/v)n-octyl beta-D-glucoside, 0.1 M Tris-HCl, pH 7.0, vapor diffusion, hanging drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.25 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 248.96 | ¦Á = 90 |
b = 50.46 | ¦Â = 93.66 |
c = 50.77 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 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 | ADSC QUANTUM 4 | 2009-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.933 | ESRF | ID14-2 |
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 | 1.9 | 50 | 99.1 | 0.045 | 16.46 | 50017 | 49556 | -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 | 1.9 | 1.95 | 95.6 | 0.497 | 2.1 |
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 2QPM | 1.9 | 20 | 47034 | 2475 | 100 | 0.21846 | 0.21658 | 0.25518 | RANDOM | 33.567 |
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] | |
-2.58 | -0.31 | 2.52 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.413 |
r_dihedral_angle_4_deg | 15.217 |
r_dihedral_angle_3_deg | 13.439 |
r_dihedral_angle_1_deg | 5.304 |
r_scangle_it | 1.727 |
r_scbond_it | 1.024 |
r_angle_refined_deg | 0.987 |
r_mcangle_it | 0.883 |
r_mcbond_it | 0.473 |
r_chiral_restr | 0.064 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3783 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms | 202 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DNA | data collection |
XDS | data reduction |