3L0K
Human orotidyl-5'-monophosphate decarboxylase in complex with 6-acetyl-UMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 300 | 0.1M Tris-HCl pH 8.0, 1.8M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0 K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.76 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 70.53 | ¦Á = 90 |
b = 61.89 | ¦Â = 112.54 |
c = 70.14 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARMOSAIC 225 mm CCD | 2008-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0000 | SLS | X10SA |
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 | 1.34 | 42.52 | 99.7 | 0.052 | 11.9 | 3.6 | 119377 |
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) | |||||||||||
1.34 | 1.36 | 90.3 | 0.348 | 2.4 | 2.5 | 3443 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.34 | 42.52 | 119377 | 6349 | 98.08 | 0.1274 | 0.12657 | 0.14271 | RANDOM | 14.031 |
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] | |
4.66 | 10.9 | -9.3 | 4.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.14 |
r_dihedral_angle_4_deg | 17.084 |
r_dihedral_angle_3_deg | 12.836 |
r_rigid_bond_restr | 12.371 |
r_sphericity_free | 7.239 |
r_dihedral_angle_1_deg | 5.919 |
r_sphericity_bonded | 4.868 |
r_angle_refined_deg | 1.332 |
r_angle_other_deg | 0.915 |
r_mcbond_it | 0.112 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4161 |
Nucleic Acid Atoms | |
Solvent Atoms | 599 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |