3TSL
Crystal structure of M-PMV DUTPASE relaxed end-product (dUMP) complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2D4L | PDB ENTRY 2D4L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.833 | α = 90 |
b = 60.833 | β = 90 |
c = 64.043 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | MAR CCD 165 mm | MIRRORS | 2005-01-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8034 | EMBL/DESY, HAMBURG | X13 |
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 | 2.2 | 20 | 90.3 | 0.063 | 10.3 | 1.9 | 6238 | 6238 | -3 |
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 | 2.2 | 2.31 | 90.3 | 0.289 | 2.6 | 1.8 | 844 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | RIGID BODY REFINEMENT | THROUGHOUT | PDB ENTRY 2D4L | 2.2 | 20 | 6166 | 5833 | 333 | 89.35 | 0.19545 | 0.19343 | 0.22942 | RANDOM | 30.524 |
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] | |
1.09 | 0.55 | 1.09 | -1.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 43.634 |
r_dihedral_angle_4_deg | 30.593 |
r_dihedral_angle_3_deg | 16.957 |
r_scangle_it | 7.228 |
r_dihedral_angle_1_deg | 6.958 |
r_scbond_it | 5.012 |
r_angle_refined_deg | 1.704 |
r_mcangle_it | 1.315 |
r_mcbond_it | 0.688 |
r_chiral_restr | 0.1 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 804 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | phasing |