3Q91
Crystal Structure of Human Uridine Diphosphate Glucose Pyrophosphatase (NUDT14)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1G0S | PDB entries 1G0S, 1VIQ, 1VIU and 2DSB |
experimental model | PDB | 1VIQ | PDB entries 1G0S, 1VIQ, 1VIU and 2DSB |
experimental model | PDB | 1VIU | PDB entries 1G0S, 1VIQ, 1VIU and 2DSB |
experimental model | PDB | 2DSB | PDB entries 1G0S, 1VIQ, 1VIU and 2DSB |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 20 % w/v PEG3350, 0.2 M AMMONIUM FORMATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.04 | α = 90 |
b = 106.24 | β = 90 |
c = 106.35 | γ = 90 |
Symmetry | |
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Space Group | P 2 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-225 | MIRRORS | 2009-06-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.91841 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.7 | 53.17 | 99.7 | 0.063 | 0.063 | 8.5 | 4.8 | 26804 | 26724 | -3 | 83.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.7 | 2.85 | 99.5 | 0.708 | 0.708 | 2.1 | 4.8 | 3827 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 entries 1G0S, 1VIQ, 1VIU and 2DSB | 2.7 | 53.17 | 25328 | 1376 | 99.53 | 0.23054 | 0.22844 | 0.27137 | RANDOM | 68.955 |
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] | |
4.87 | -2.13 | -2.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.676 |
r_dihedral_angle_3_deg | 15.718 |
r_dihedral_angle_4_deg | 12.61 |
r_dihedral_angle_1_deg | 6.158 |
r_scangle_it | 1.438 |
r_angle_refined_deg | 1.068 |
r_scbond_it | 0.84 |
r_angle_other_deg | 0.767 |
r_mcangle_it | 0.628 |
r_mcbond_it | 0.322 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4399 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |