2O55
Crystal Structure of a putative glycerophosphodiester phosphodiesterase from Galdieria sulphuraria
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (0.90 M lithium sulfate, 0.10 M sodium succinate pH 4), Cryoprotected with: well solution supplemented with up to 20% glycerol, vapor diffusion, hanging drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 53.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.427 | α = 90 |
b = 102.427 | β = 90 |
c = 51.709 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2006-11-08 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97923, 0.96400 | APS | 23-ID-D |
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 | 2.8 | 36.387 | 97.4 | 0.099 | 15.064 | 12.7 | 7690 |
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 | 2.8 | 2.9 | 82.5 | 0.197 | 4.527 | 4.6 | 631 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.806 | 36.387 | 7678 | 352 | 97.412 | 0.195 | 0.192 | 0.255 | RANDOM | 17.983 |
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] | |
1.506 | 0.753 | 1.506 | -2.258 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.546 |
r_dihedral_angle_3_deg | 20.807 |
r_dihedral_angle_4_deg | 19.714 |
r_dihedral_angle_1_deg | 8.242 |
r_scangle_it | 2.251 |
r_angle_refined_deg | 1.486 |
r_scbond_it | 1.363 |
r_mcangle_it | 0.844 |
r_mcbond_it | 0.46 |
r_nbtor_refined | 0.316 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2045 |
Nucleic Acid Atoms | |
Solvent Atoms | 1 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |