3ELO
Crystal Structure of Human Pancreatic Prophospholipase A2
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.4 | 298 | 0.1M Tris, 0.2M lithium sulfate, 33% PEG 4000, pH 8.4, vapor diffusion, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.88 | 34.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.549 | α = 90 |
b = 56.549 | β = 90 |
c = 60.631 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | 110 | CCD | OXFORD RUBY CCD | 2007-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCED ULTRA | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.55 | 18.683 | 99.9 | 0.072 | 0.072 | 7.879 | 5.2 | 16060 |
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) | ||||||||||
1 | 1.55 | 1.63 | 100 | 0.513 | 0.513 | 1.4 | 3.8 | 2323 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.55 | 18.68 | 16042 | 810 | 99.99 | 0.147 | 0.145 | 0.183 | RANDOM | 8.896 |
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] | |
0.06 | 0.03 | 0.06 | -0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.676 |
r_dihedral_angle_3_deg | 11.998 |
r_dihedral_angle_4_deg | 9.309 |
r_dihedral_angle_1_deg | 5.789 |
r_scangle_it | 2.571 |
r_scbond_it | 1.611 |
r_angle_refined_deg | 1.365 |
r_angle_other_deg | 0.936 |
r_mcangle_it | 0.915 |
r_mcbond_it | 0.524 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1033 |
Nucleic Acid Atoms | |
Solvent Atoms | 164 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrysalisPro | data reduction |