3UD6
Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.5 | 298 | Protein at 5mg/ml in 100mm NaCl, 25mm TRIS pH7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mN Na acetate pH5.5, vapor diffusion, temperature 298k, VAPOR DIFFUSION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.684 | α = 90 |
b = 62.684 | β = 90 |
c = 123.68 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | VARIMAX HF | 2009-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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) | 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 | 2.091 | 50 | 99 | 0.037 | 22 | 2.9 | 17137 | 2 | 29.82 |
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) | |||||||||||
1 | 2.091 | 2.16 | 95.2 | 0.153 | 6.86 | 2.3 |
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 1A53, MODIFIED TO PREVENT MODEL BIAS | 2.091 | 19.47 | 16229 | 868 | 99.3 | 0.227 | 0.227 | 0.258 | RANDOM | 32.85 |
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] | |
-0.01 | -0.01 | -0.01 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.439 |
r_dihedral_angle_4_deg | 16.778 |
r_dihedral_angle_3_deg | 15.268 |
r_dihedral_angle_1_deg | 4.933 |
r_scangle_it | 3.215 |
r_scbond_it | 1.908 |
r_mcangle_it | 1.376 |
r_angle_refined_deg | 1.028 |
r_mcbond_it | 0.765 |
r_nbtor_refined | 0.299 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1995 |
Nucleic Acid Atoms | |
Solvent Atoms | 65 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |