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. 2016 Feb 8;55(9):1384–1397. doi: 10.1021/acs.biochem.5b00838

Table 1. Data Collection and Refinement Statistics.

  INPP5B  
  BiPh(3,3′,4,4′,5,5′)P6 Bz(1,2,4,5)P4
PDB ID 5A7I 5A7J
Data Collection
synchrotron BESSY BESSY
beamline BL14.1 BL14.1
wavelength (Å) 0.91841 0.91841
resolution range (Å) 34.29–2.89 48.48–2.90
(outest shell) (3.05–2.89) (3.06–2.9)
space group P41212 P21
unit-cell dimensions (Å) a = 96.97 a = 52.26
  b = 96.97 b = 94.44
  c = 152.14 c = 78.31
unit-cell angles (deg) α = β = γ = 90 α = γ = 90, β = 106.32
completeness (%) 99.9 (100.0) 99.7 (99.7)
unique reflections 16922 16223
mean (I)/SD (I)a 21.2 (2.2) 6.9 (2.3)
redundancy 7.0 (7.2) 3.6 (3.6)
Rmeas (%)b 7.5 (90.7) 19.4 (67.9)
Refinement
resolution range (Å) 34.29–2.89 48.48–2.90
(outest shell) (2.97–2.89) (3.10–2.90)
Rcryst (%)c 19.8 (33.8) 20.2 (21.9)
Rfree (%)d 22.3 (34.5) 25.0 (31.0)
Model Content
protein atoms 2545 4971
ligand atoms 42 52
metal atoms 1 0
water molecules 28 76
others 16 26
average B factors (Å2)    
protein atoms 83.59 39.10
ligand atoms 76.44 65.84
metal atoms 66.37 n.d.
water molecules 71.94 19.15
other atoms 111.59 63.89
r.m.s.d. bonds (Å) 0.007 0.008
r.m.s.d. angles (deg) 1.191 1.000
Ramachandran plot (%)e    
(favored, outliers) 95.82, 0.32 94.95, 0
a

Mean (I)/SD is the mean ratio for all reflections of ⟨Ih⟩/SD ⟨Ih⟩, where for each unique reflection h, ⟨Ih⟩ is the weighted mean of measured Ih, and SD ⟨Ih⟩ is the mean of estimated error SD(I).

b

Rmeas = Inline graphic

c

Rcryst = Inline graphic, where Fobs and Fcalc are the observed and calculated structure factors, respectively.

d

Rfree is the same as Rcryst but based on a subset of 5% (5.1% and 5.0% for INPP5B-BiPh(3,3′,4,4′,5,5′)P6 and INPP5B-Bz(1,2,4,5)P4, respectively) of reflections omitted during refinement.

e

Values were computed by Molprobity (ref (26)).