3GB9
Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoroadenine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RFG | PDB entry 1RFG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 298 | 1.54 M Ammonium sulfate, 0.05M Sodium potassium phosphate pH 6.8, 3% Trimethylamine N-oxide, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.39 | 63.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.791 | α = 90 |
b = 130.648 | β = 90 |
c = 149.177 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 QUANTUM 315 | 2008-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9793 | APS | 24-ID-C |
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 | 2.3 | 50 | 81.2 | 0.105 | 16.923 | 5.8 | 51620 | -3 | 52.4 |
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 | 2.3 | 2.38 | 26.8 | 0.336 | 5.4 | 1680 |
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 1RFG | 2.3 | 50 | 51499 | 2605 | 81.6 | 0.186 | 0.184 | 0.227 | RANDOM | 32.774 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
5.22 | -2.57 | -2.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.966 |
r_dihedral_angle_4_deg | 18.949 |
r_dihedral_angle_3_deg | 17.336 |
r_dihedral_angle_1_deg | 6.189 |
r_scangle_it | 3.637 |
r_mcangle_it | 3.566 |
r_scbond_it | 2.49 |
r_mcbond_it | 2.168 |
r_angle_refined_deg | 1.362 |
r_angle_other_deg | 0.86 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6452 |
Nucleic Acid Atoms | |
Solvent Atoms | 211 |
Heterogen Atoms | 204 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |