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Table 1 Summary of crystallographic data and refinement statistics

From: Structural insights into Noonan/LEOPARD syndrome-related mutants of protein-tyrosine phosphatase SHP2 (PTPN11)

Parameters Wild type D61G E139D Y279C N308D Q506P
Data collection:
Resolution, (Å) 2.75 2.20 2.45 2.10 2.10 2.70
Outermost resolution shell, (Å) (2.85-2.75) (2.30-2.20) (2.55-2.45) (2.20-2.10) (2.20-2.10) (2.80-2.70)
Space group P21 P21212 P212121 P21 P212121 P21212
Unit cell parameters
a, (Å) 55.7 55.0 56.3 55.7 55.9 54.8
b, (Å) 211.7 220.3 212.4 212.0 211.2 202.4
c, (Å) 91.2 41.7 92.2 46.0 91.6 44.5
β, (°) 89.97    96.6   
Molecules per asymmetric unit 4 1 2 2 2 1
Unique reflections 53,849 26,689 41,625 61,515 64,401 14,342
Multiplicity 3.1 (3.4) 6.3 (6.1) 6.5 (6.3) 3.5 (3.5) 7.0 (7.2) 6.5 (6.3)
Average I/σ (I) 5.5 (2.2) 11.1 (2.7) 9.2 (2.3) 6.9 (1.9) 11.0 (3.2) 12.0 (2.8)
R merge , (%) 18.9 (46.0) 10.6 (52.0) 11.4 (57.1) 10.4 (49.7) 9.4 (43.0) 13.9 (56.0)
Completeness, (%) 95.9 (98.5) 99.3 (96.2) 99.7 (98.1) 99.9 (99.6) 99.9 (100) 99.9 (100)
Refinement and structure statistics
R work , (%) 25.6 21.1 21.3 21.1 24.2 22.7
R free , (%) 28.5 23.3 25.4 24.3 28.7 24.2
RMSD from ideal geometry
Bond lengths, (Å) 0.007 0.007 0.010 0.008 0.009 0.007
Bond angles, (°) 0.91 0.99 1.24 1.00 1.10 0.91
Numbers of atoms
Protein (non-hydrogen) 15,560 4,021 8,214 8,013 8,100 3,951
Water oxygen atoms 784 134 365 261 679 54
Ligand’s atoms   20   90   36
PDB ID 4NXD 4H10 4NWG 4GWF 4NWF 4H34
  1. R merge  = ∑  hkl |I − 〈I〉|/∑ hkl I, where I is the intensity of the individual reflections.
  2. R work  = ∑ |F obs  − F cal |/∑|F obs , where Fobs and Fcalc are the observed and the calculated structure factors, respectively.
  3. R free was calculated using 5% of total reflections randomly chosen and excluded from the crystallographic refinement.