4X90
Crystal structure of Lysosomal Phospholipase A2
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 100 mM HEPES pH 7.5, 3.5% PEG 8000, 28% MPD, 300 mM (NH4)2HPO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.28 | 62.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.806 | α = 78.13 |
b = 91.151 | β = 88.46 |
c = 100.266 | γ = 88.5 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2013-06-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97937 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.83 | 30 | 97.8 | 0.095 | 6.7 | 4 | 183439 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.83 | 1.86 | 96.4 | 0.631 | 3.9 | 8966 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.84 | 30 | 174210 | 9229 | 96.85 | 0.155 | 0.1541 | 0.1733 | RANDOM | 26.422 |
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] | |
1.71 | -0.24 | 0.13 | -0.22 | 0.2 | -1.3 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.364 |
r_dihedral_angle_4_deg | 13.245 |
r_dihedral_angle_3_deg | 11.529 |
r_dihedral_angle_1_deg | 5.816 |
r_mcangle_it | 2.04 |
r_angle_refined_deg | 1.441 |
r_mcbond_it | 1.271 |
r_mcbond_other | 1.271 |
r_angle_other_deg | 1.168 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12076 |
Nucleic Acid Atoms | |
Solvent Atoms | 1065 |
Heterogen Atoms | 476 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |