1R3T
Uroporphyrinogen Decarboxylase single mutant D86G in complex with coproporphyrinogen-III
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 6.5 | 294 | PBG, PBG-D and U3S were added to the protein solution in an anaerobic chamber. URO-D was active under these conditions, converting uro'gen-III to cop'gen-III. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.68 | α = 90 |
b = 102.68 | β = 90 |
c = 73.13 | 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 | 1.7 | 87.71 | 96 | 0.096 | 0.096 | 13 | 4.9 | 47218 | 47218 |
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 | 1.7 | 1.76 | 88 | 0.232 | 0.232 | 2.7 | 4.9 |
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 | 1.7 | 87.71 | 47218 | 45924 | 1187 | 95.76 | 0.17019 | 0.17019 | 0.16944 | 0.20004 | RANDOM | 22.484 |
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] | |
-1.05 | -0.53 | -1.05 | 1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.615 |
r_scangle_it | 4.062 |
r_scbond_it | 2.515 |
r_mcangle_it | 1.641 |
r_angle_refined_deg | 1.547 |
r_mcbond_it | 0.959 |
r_angle_other_deg | 0.887 |
r_symmetry_hbond_refined | 0.352 |
r_symmetry_vdw_refined | 0.334 |
r_symmetry_vdw_other | 0.316 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2794 |
Nucleic Acid Atoms | |
Solvent Atoms | 361 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |