3HSW
Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with 2-methoxycyclohexa-2-5-diene-1,4-dione
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1P2P | PDB ENTRY 1P2P |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 294 | 15% MPD, 0.05M Tris Maleate, 5mM Calcium Chloride, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.38 | 63.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.36 | α = 90 |
b = 68.36 | β = 90 |
c = 70.12 | 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 | IMAGE PLATE | MAR scanner 345 mm plate | Mirrors | 2009-03-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.542 |
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 | 2.5 | 45.24 | 97.3 | 0.073 | 0.065 | 8.5 | 6789 | 6759 | 2.5 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.5 | 2.64 | 70.79 | 0.073 | 0.065 | 955 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 1P2P | 2.5 | 13.65 | 2 | 2.5 | 6811 | 6356 | 349 | 98.44 | 0.2303 | 0.18214 | 0.17965 | 0.22883 | RANDOM | 23.783 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.295 |
r_dihedral_angle_4_deg | 28.049 |
r_dihedral_angle_3_deg | 22.792 |
r_dihedral_angle_1_deg | 7.137 |
r_scangle_it | 4.224 |
r_scbond_it | 2.545 |
r_angle_refined_deg | 2.079 |
r_mcangle_it | 1.644 |
r_mcbond_it | 0.84 |
r_chiral_restr | 0.135 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 971 |
Nucleic Acid Atoms | |
Solvent Atoms | 32 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
Auto | model building |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
Auto | phasing |