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. 2008 Oct 31;283(44):30351–30362. doi: 10.1074/jbc.M803316200

TABLE 2.

Summary of structure statistics for PLCγ2 spPH

<SA> represents the set of 20 selected lowest energy conformers obtained by restrained dynamical simulated annealing in CNS. SAlowest refers to the lowest energy structure of the set. There were no NOE (>0.4 Å) or dihedral (>5°) violations for any of the lowest energy conformers.

<SA> SAlowest
Experimental restraintsa
All (Å) (2487) 0.018 ± 0.002 0.014
Intraresidue (786) 0.014 ± 0.003 0.010
Sequential (553) 0.014 ± 0.005 0.010
Short (373) 0.023 ± 0.003 0.020
Long (766) 0.018 ± 0.001 0.015
Ambiguous (9) 0.009 ± 0.005 0.009
Hydrogen bond restraints (Å) (70) 0.031 ± 0.004 0.029
Dihedral angle restraints (degrees) (114) 0.26 ± 0.03 0.236
Deviations from idealized covalent geometryb
Bonds (Å) (1930) 0.0013 ± 0.0001 0.0012
Angles (degrees) (3490) 0.31 ± 0.004 0.31
Improper dihedrals (degrees) (1020) 0.2 ± 0.01 0.2
Structural statistics for the ensemblec
PROCHECK parameters
Most favored region (%) 73.1 ± 2.7 74.3
Additionally allowed (%) 22.5 ± 2.7 23.8
Generously allowed (%) 3.0 ± 1.6 1.0
Disallowed (%) 1.5 ± 0.7 1.0
Number of bad contacts 3 ± 2 1
Root mean square difference from the average structured
Backbone (N, Cα, C) (Å) 0.41 ± 0.05 0.34
Heavy atoms (Å) 0.76 ± 0.06 0.62
a

Sum averaging of NOE distance restraints was used for groups with degenerate proton chemical shifts. The interproton unambiguous distance restraint list comprised 786 intraresidue, 553 sequential (|i - j| = 1|), 373 short range (1 < |i - j| < 5), and 776 long range (|i - j| > 5). Hydrogen bond restraints were applied as pairs of distance restraints: HN···O, 1.2-2.2 Å; N···O, 1.2-3.2 Å. The final values for the respective force constants were as follows: NOE, 30 kcal mol−1 Å−2; hydrogen bonds, 50 kcal mol−1 Å−2; dihedral angles, 200 kcal mol−1 rad−2.

b

The final values for the respective force constants were as follows: bond lengths, 1000 kcal mol−1 Å−2; angles and improper torsions, 500 kcal mol−1 rad−2; the improper torsion angle restraints serve to maintain planarity and chirality.

c

The program PROCHECK (64) was used to assess the stereochemical parameters of the family of conformers for the spPH. The figures indicate the percentage of residues with backbone Φ and Ψ angles in separate regions of the Ramachandran plot, defined in the program. The number of bad contacts per 100 residues is expected to be in the range 0 - 30 for protein crystal structures of better than 3.0 Å resolution.

d

The precision of the atomic coordinates is defined as the average pairwise root mean square difference between each of the 20 conformers and a mean coordinate structure SA generated by iterative best fit of the backbone atoms (N, Cα, and C) over residues 478 - 508 and 849 - 908 of PLCγ2spPH (comprising the core secondary structure elements and omitting the flexible N and C termini and the disordered loop between β3 and β4), followed by coordinate averaging.