Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / phospholipid binding / positive regulation of MAP kinase activity / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / positive regulation of immune response / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.089 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24935
295
4.7 %
RANDOM
Rwork
0.19137
-
-
-
obs
0.19411
5654
91.13 %
-
all
-
6866
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 40.616 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
971
0
20
58
1049
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.022
1017
X-RAY DIFFRACTION
r_angle_refined_deg
1.898
1.95
1373
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.62
5
123
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
44.918
25
50
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.131
15
163
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
26.11
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.132
0.2
138
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
783
X-RAY DIFFRACTION
r_mcbond_it
1.048
1.5
619
X-RAY DIFFRACTION
r_mcangle_it
2.062
2
993
X-RAY DIFFRACTION
r_scbond_it
2.906
3
398
X-RAY DIFFRACTION
r_scangle_it
5.023
4.5
380
LS refinement shell
Resolution: 2.502→2.566 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.265
25
-
Rwork
0.25
468
-
obs
-
-
100 %
+
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