2G06
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, with bound magnesium(II)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BDU | pdb entry 2BDU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED FOR 15 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.98 | 58.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 134.343 | α = 90 |
b = 134.343 | β = 90 |
c = 39.152 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 | BRUKER PROTEUM-R | MONTEL OPTICS | 2006-01-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
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 | 2.25 | 67.17 | 100 | 0.1006 | 20.61 | 17.82 | 37523 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.25 | 2.3 | 100 | 0.6371 | 2.67 | 6.47 | 2423 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2BDU | 2.25 | 67.17 | 37505 | 1899 | 99.955 | 0.158 | 0.158 | 0.1548 | 0.2193 | RANDOM | 35.072 |
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] | |
0.204 | 0.102 | 0.204 | -0.307 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.774 |
r_dihedral_angle_4_deg | 22.555 |
r_dihedral_angle_3_deg | 15.516 |
r_scangle_it | 5.969 |
r_dihedral_angle_1_deg | 5.893 |
r_scbond_it | 4.389 |
r_mcangle_it | 2.236 |
r_angle_refined_deg | 1.474 |
r_mcbond_it | 1.291 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4652 |
Nucleic Acid Atoms | |
Solvent Atoms | 815 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
SAINT | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SAINT | data reduction |
SADABS | data scaling |
MOLREP | phasing |