1Z4L
Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with thymidine 5'-monophosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.5 | pH 4.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 55 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 73.646 | ¦Á = 90 |
b = 73.646 | ¦Â = 90 |
c = 106.375 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | 2004-01-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 |
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 | 1.8 | 40 | 99.4 | 0.056 | 17.7 | 4.9 | 27554 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.8 | 1.86 | 99.4 | 0.35 | 3.9 |
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 | 1.8 | 40 | 26138 | 1386 | 99.49 | 0.17438 | 0.1725 | 0.21016 | RANDOM | 19.26 |
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] | |
-0.36 | -0.36 | 0.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.45 |
r_scangle_it | 4.409 |
r_scbond_it | 2.767 |
r_mcangle_it | 2.007 |
r_angle_refined_deg | 1.79 |
r_angle_other_deg | 1.281 |
r_mcbond_it | 1.144 |
r_symmetry_vdw_other | 0.337 |
r_nbd_other | 0.254 |
r_nbd_refined | 0.222 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1602 |
Nucleic Acid Atoms | |
Solvent Atoms | 196 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |