2YB0
The Crystal Structure of Leishmania major dUTPase in complex deoxyuridine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CJE | PDB ENTRY 2CJE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1 M NACL, 0.1 M BIS-TRIS PH 6.5, 1.5 M (NH4)2SO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.29 | 71.32 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 109.186 | ¦Á = 90 |
b = 109.186 | ¦Â = 90 |
c = 308.882 | ¦Ã = 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 | CCD | ADSC CCD | 2009-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.28 | 60.8 | 100 | 0.11 | 17.4 | 13.5 | 98557 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.28 | 2.4 | 99.8 | 0.71 | 3 | 10.5 |
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 2CJE | 2.28 | 54.59 | 93350 | 4921 | 100 | 0.211 | 0.21 | 0.235 | RANDOM | 85.96 |
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] | |
0.35 | 0.18 | 0.35 | -0.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.975 |
r_dihedral_angle_4_deg | 16.041 |
r_dihedral_angle_3_deg | 14.449 |
r_scangle_it | 8.159 |
r_scbond_it | 6.755 |
r_dihedral_angle_1_deg | 5.317 |
r_mcangle_it | 4.382 |
r_mcbond_it | 3.075 |
r_angle_refined_deg | 1.25 |
r_mcbond_other | 1.189 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8004 |
Nucleic Acid Atoms | |
Solvent Atoms | 97 |
Heterogen Atoms | 109 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |