1R3R
Uroporphyrinogen Decarboxylase with mutation D86N
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 6.5 | 294 | The crystal trial was conducted in an anaerobic chamber, with PBG, PBG-D added to the solution. These conditions are conducive to formation of an enzyme product complex, as the enzyme is typically active under these conditions (see related strcuture 1R3Q). There is not a ligand bound in this structure. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 47.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.735 | α = 90 |
b = 102.735 | β = 90 |
c = 73.426 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IIC | 2003-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.85 | 87.71 | 96 | 0.083 | 0.083 | 9 | 5 | 36928 | 36928 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.85 | 1.92 | 80 | 0.437 | 0.437 | 2.8 | 5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | FOURIER SYNTHESIS | THROUGHOUT | 1URO | 1.85 | 87.71 | 36928 | 35762 | 1122 | 95.81 | 0.16212 | 0.16212 | 0.16117 | 0.19242 | RANDOM | 20.283 |
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] | |
-1.53 | -0.77 | -1.53 | 2.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.737 |
r_scangle_it | 5.177 |
r_scbond_it | 3.091 |
r_mcangle_it | 2.019 |
r_angle_refined_deg | 1.69 |
r_mcbond_it | 1.119 |
r_angle_other_deg | 0.961 |
r_symmetry_vdw_refined | 0.42 |
r_symmetry_vdw_other | 0.353 |
r_nbd_other | 0.25 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2989 |
Nucleic Acid Atoms | |
Solvent Atoms | 381 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |