Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 3
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Sample preparation
Crystal
Density Matthews: 1.9 Å3/Da / Density % sol: 35.24 % / Description: NONE
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.2 M AMMONIUM SULFATE, 1.0 M SODIUM CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM DEUTERIUM PHOSPHATE, PH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE 295 K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.96
1
2
1.3
1
Reflection
Resolution: 1.6→13.28 Å / Num. obs: 10605 / % possible obs: 0.5 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 11.79 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.6
Reflection shell
Resolution: 1.6→1.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 0.7 / % possible all: 0.1
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
d*TREK
datareduction
d*TREK
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.6→13.285 Å / SU ML: 0.53 / σ(F): 0 / Phase error: 35.38 / Stereochemistry target values: ML Details: THIS STRUCTURE REPRESENTS A TRANSIENT STATE PROTEIN ENTERS UPON BLUE LIGHT ACTIVATION, PERSISTING FOR 600 PICOSECONDS.
Rfactor
Num. reflection
% reflection
Rfree
0.2928
397
4 %
Rwork
0.2211
-
-
obs
0.2239
10036
72.37 %
Solvent computation
Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.927 Å2 / ksol: 0.114 e/Å3
Displacement parameters
Biso mean: 20.3 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.1216 Å2
0 Å2
0 Å2
2-
-
-0.1216 Å2
0 Å2
3-
-
-
0.2432 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→13.285 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
976
0
11
80
1067
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
1009
X-RAY DIFFRACTION
f_angle_d
1.189
1359
X-RAY DIFFRACTION
f_dihedral_angle_d
16.068
367
X-RAY DIFFRACTION
f_chiral_restr
0.075
140
X-RAY DIFFRACTION
f_plane_restr
0.007
180
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.6001-1.8312
0.4422
92
0.3651
2404
X-RAY DIFFRACTION
55
1.8312-2.3051
0.3137
154
0.2611
3584
X-RAY DIFFRACTION
81
2.3051-13.2851
0.2521
151
0.1742
3651
X-RAY DIFFRACTION
81
+
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