6HML
POLYADPRIBOSYL GLYCOSIDASE IN COMPLEX WITH PDD00017299
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4A0D |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | Mix 750 nL purified protein at 7.5 mg per mL in 50mM HEPES, pH 7.0, 150 mM NaCl, 2mM DTT with 250 nL of seed stock and 1000 nL of a precipitant consisting of 18-23 percent PEG 3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5. Seed stock was prepared using a Seed Bead from a co-crystal with ADP-ribose, with co-crystallisation mother liquor (19 percent PEG 3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5) as the stabilising solution |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.31 | α = 90 |
b = 90.19 | β = 90 |
c = 95.99 | 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 | PIXEL | DECTRIS PILATUS3 6M | 2013-08-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.979 | Diamond | I04 |
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 | 67.31 | 99.9 | 0.083 | 15.2 | 6.4 | 28396 | 47.59 |
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 | 2.25 | 2.31 | 99.9 | 0.758 | 2.7 | 6.6 |
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 | 4A0D | 2.25 | 67.31 | 28343 | 1429 | 99.84 | 0.1639 | 0.1622 | 0.1965 | RANDOM | 47.88 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
9.6477 | 0.5073 | -10.155 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
BOND LENGTHS | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4003 |
Nucleic Acid Atoms | |
Solvent Atoms | 325 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
BUSTER | refinement |
PHASER | phasing |