3FUC
Recombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate analogue inhibitor 9-(5',5'-difluoro-5'-phosphonopentyl)-9-deazaguanine structure in a new space group with one full trimer in the asymmetric unit
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.7 | 298 | 33% PEG 400, 0.1M SODIUM AZIDE, 0.1M HEPES, 0.1M MAGNESIUM CHLORIDE, 1% OCTYL BETA-D-GLUCOPYRANOSIDE, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 135.795 | α = 90 |
b = 78.253 | β = 97.19 |
c = 94.901 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | MARRESEARCH | BENT MIRROR | 2007-08-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | 1.0500 | MPG/DESY, HAMBURG | BW6 |
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 | 1.45 | 10 | 99.4 | 0.082 | 4.4 | 3.3 | 173360 | 173360 | 16 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.45 | 1.53 | 99.9 | 0.236 | 3 | 2.6 | 25329 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1LVU | 1.45 | 10 | 173360 | 173360 | 8787 | 99.31 | 0.18095 | 0.18095 | 0.17999 | 0.19933 | THIN RESIOLUTION SHELLS | 16.41 |
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] | |
-0.05 | 0.13 | -0.26 | 0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.674 |
r_dihedral_angle_4_deg | 17.384 |
r_dihedral_angle_3_deg | 13.148 |
r_dihedral_angle_1_deg | 5.847 |
r_angle_other_deg | 3.683 |
r_scangle_it | 3.264 |
r_scbond_it | 2.071 |
r_angle_refined_deg | 1.386 |
r_mcangle_it | 1.369 |
r_mcbond_it | 0.782 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6456 |
Nucleic Acid Atoms | |
Solvent Atoms | 447 |
Heterogen Atoms | 72 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |