Table 1 Summary of the intensity quantification of the difference Fourier electron density map for key water molecules, chloride ions, and residues.

Values given in units of σ (equal to the root mean square electron density of the unit cell). Values below ±3.0σ were set to zero, as being of too low significance. Cells are colored according to the σ value, being darker green when the magnitude of the measured difference is stronger. Residue nomenclature: SC, side chain; BB, back bone; (+), positive density feature; (−), negative density feature.

DatasetsCW95K-ND3CW95K-ND10CW95K-ND30Pulse-95KPulse-140K
S/D (e.A3/s)0.0060.0120.0160.0090.016
Retinal
  C14/C15 (+)5.47.66.99.36.1
  C14/C15 (−)−5.9−7.0−5.2−9.2−4.3
  C20 (+)4.33.94.44.94.8
  C20 (−)−3.5−4.5−5.4−5.8−4.2
Lys235
  Nz/CE (+)11.09.88.510.94.9
  Nz/CE (−)−13.4−16.8−11.4−15.3−7.2
  CD (+)3.53.60.04.30.0
  CD (−)−7.1−7.5−3.8−7.6−3.8
  CG (+)0.03.83.154.70.0
  CG (−)0.0−6.00.0−6.60.0
  BB (+)3.34.50.04.60.0
  BB (−)−4.1−4.7−3.4−4.5−4.5
Ser234
  SC (+)3.07.17.13.53.6
  SC (−)−4.2−6.6−6.0−4.1−3.6
  BB (+)3.74.53.44.83.0
  BB (−)−4.4−4.8−3.5−6.20.0
Asp231
  SC (+)4.36.27.08.15.0
  SC (−)−9.1−11.4−9.8−13.0−10.4
  BB (+)0.00.00.03.93.5
  BB (−)0.0−4.6−4.2−5.1−4.4
Arg95
  SC (+)0.00.04.94.14.1
  SC (−)−3.8−3.9−5.4−4.6−4.3
Cys105
  SC (+)3.24.65.54.44.5
  SC (−)−5.2−5.8−6.4−5.1−5.6
His29
  SC (+)3.44.96.15.46.4
  SC (−)0.0−4.8−5.3−5.9−7.0
  BB (+)0.00.04.90.03.5
  BB (−)0.00.0−3.20.00.0
Met58
  SC (+)3.34.84.74.93.6
  SC (−)−5.5−9.2−9.0−9.8−7.3
Trp99
  SC (+)0.03.53.80.00.0
  SC (−)0.0−3.8−4.20.00.0
Trp201
  SC (+)3.63.26.14.1.4.0
  SC (−)−3.9−4.5−6.1−3.9−5.4
Asn168
  SC (+)3.33.24.43.23.5
  SC (−)−4.4−3.4−5.1−4.2−5.5
Water
  W4 (+)0.00.05.60.00.0
  W4 (−)0.0−3.9−5.10.00.0
  W7 (+)0.05.03.04.10.0
  W7 (−)−4.1−5.0−5.8−4.7−4.7
Cl ion
  Cl-1 (−)−9.8−9.6−11.3−9.8−8.7
  Cl-1B (+)4.95.15.14.14.7
  Cl-3 (+)3.63.40.00.00.0
  Cl-4 (+)0.03.87.60.04.9
  Cl-5 (+)3.84.54.64.23.8
  Cl-6 (+)4.04.66.75.33.4