3QLM
Crystal structure of porcine pancreatic phospholipase A2 in complex with n-hexadecanoic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3O4M |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 294 | 15% MPD, 0.05M Tris Maliate, 5mM Calcium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.44 | 64.27 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 69.26 | α = 90 |
b = 69.26 | β = 90 |
c = 69.66 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 2 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 | IMAGE PLATE | MAR scanner 345 mm plate | Mirrors | 2010-02-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.542 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 45.44 | 90.4 | 0.079 | 0.084 | 6866 | 6010 | 2.6 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.6 | 2.74 | 90.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 3O4M | 2.5 | 15 | 6866 | 5654 | 295 | 91.13 | 0.19411 | 0.19137 | 0.24935 | RANDOM | 40.616 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 44.918 |
r_dihedral_angle_4_deg | 26.11 |
r_dihedral_angle_3_deg | 20.131 |
r_dihedral_angle_1_deg | 6.62 |
r_scangle_it | 5.023 |
r_scbond_it | 2.906 |
r_mcangle_it | 2.062 |
r_angle_refined_deg | 1.898 |
r_mcbond_it | 1.048 |
r_chiral_restr | 0.132 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 971 |
Nucleic Acid Atoms | |
Solvent Atoms | 58 |
Heterogen Atoms | 20 |
Software
Software | |
---|---|
Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |