3NXF
Robust computational design, optimization, and structural characterization of retroaldol enzymes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1A53 | PDB ENTRY 1A53, with design and adjacent residues pared to alanine |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | Protein at 5mg/ml in 100mm NaCl, 25mm Tris pH 7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mm Na acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.916 | α = 90 |
b = 61.916 | β = 90 |
c = 121.241 | 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 | 93 | CCD | RIGAKU SATURN 944+ | Varimax HF | 2009-08-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.09 | 53.61 | 99.4 | 14.9 | 3.8 | 11053 | 10320 | 2 | 46.1 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1 | 2.09 | 2.16 | 99.9 | 0.7 | 2.07 | 3.1 | 1615 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1A53, with design and adjacent residues pared to alanine | 2.4 | 53.61 | 2 | 11023 | 10320 | 522 | 98.22 | 0.22672 | 0.22672 | 0.22454 | 0.26821 | RANDOM | 48.845 |
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] | |
1.4 | 0.7 | 1.4 | -2.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.523 |
r_dihedral_angle_3_deg | 17.172 |
r_dihedral_angle_4_deg | 13.289 |
r_dihedral_angle_1_deg | 6.527 |
r_scangle_it | 3.635 |
r_scbond_it | 2.326 |
r_mcangle_it | 1.797 |
r_angle_refined_deg | 1.375 |
r_mcbond_it | 1.011 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2000 |
Nucleic Acid Atoms | |
Solvent Atoms | 60 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |