Table 4.

Statistics for 10 lowest energy structures of Ca²⁺-RasGRP2^EF

DOI: http://dx.doi.org/10.7554/eLife.00813.026

Type of restraint		Number of restraints	Violations per structure
Total NOEs		653	0 (> 0.5 Å)
Intraresidue		221	0
Sequential NOEs		299	0
Medium-range NOEs		78	0
Long-range NOEs*		55	0
R.m.s deviations from experimental distance restraints (Å)			0.044 ± 0.0005
Hydrogen bond restraints		27
Dihedral angle restraints (ϕ, ψ and χ1)†		137	0 (>5°)
R.m.s deviations from experimental dihedral restraints (°)			0.503 ± 0.1219
Dipolar coupling restraints (Hz)‡
NH		68	0.85 ± 0.04
Cα-Hα		29	3.15 ± 0.07
Structure quality factor – overall statistics§
	Mean score	SD	Z-score
Procheck G-factor (phi/psi only)	0.07	N/A	0.59
Procheck G-factor (all dihedral angles)	−0.29	N/A	−1.71
Verify3D	0.20	0.0424	−4.17
Prosall (-ve)	0.28	0.0395	−1.53
MolProbity clashscore	30.77	3.6352	−3.75
Deviation from idealized covalent geometry
Bonds (Å)		0.0019 ± 0.00003
Angles (°)		0.3178 ± 0.0013
Impropers (°)		0.4386 ± 0.0196
Average pairwise RMSD (Å)§
All heavy atoms		1.0
Backbone heavy atoms		0.5
Ramachandran plot statistics (%)#
Most favored region		93.4
Additionally allowed region		6.6

^*Sidechains coordinating the Ca²⁺ ion in EF hands 1 and 2 were implemented as distance restraints.

^†χ¹ angles were obtained from PREDITOR (Berjanskii et al., 2006), and ϕ and ψ angles were calculated using TALOS+ (Shen et al., 2009).

^‡The r.m.s differences (Hz) between the experimental RDC data and back-calculated RDCs from the 10 lowest energy structures were obtained by SVD fitting using the program PALES (Zweckstetter and Bax, 2000).

^§The pairwise RMSD for residues 421-486 and structure quality factor were generated using the Protein Structure Validation Software suite v1.4 (Bhattacharya et al., 2007).

^#The Ramachandran statistics were evaluated for residues 422-486 with PROCHECK (Laskowski et al., 1996).