Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
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Details
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 52.5 nL drop composed of 95 mM Sodium Citrate buffer, pH 3.0, 3% polyethylene glycol 8000, 7.8% polyethylene glycol 400, 1.2% dimethyl sulfoxide, 114 mM benzamidine hydrochloride, and 5.0-10. ...Details: 52.5 nL drop composed of 95 mM Sodium Citrate buffer, pH 3.0, 3% polyethylene glycol 8000, 7.8% polyethylene glycol 400, 1.2% dimethyl sulfoxide, 114 mM benzamidine hydrochloride, and 5.0-10.0 mg/mL protein in 5 mM Tris-HCL pH 7.2 Mylar was initially used as the surface, resulting in thin polycrystalline needles. Changing the surface to COC (cyclic olefin copolymer) resulted in large high-quality single crystals.
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 10, 2019
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9202 Å / Relative weight: 1
Reflection
Resolution: 1.78→73.65 Å / Num. obs: 98773 / % possible obs: 98.3 % / Redundancy: 25.53 % / CC1/2: 0.999 / Rmerge(I) obs: 0.185 / Net I/σ(I): 10.37
Reflection shell
Resolution: 1.78→1.82 Å / Rmerge(I) obs: 0.4263 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 5726 / CC1/2: 0.476 / % possible all: 77.6
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0135
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→73.65 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.98 / SU B: 6.337 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.161
4742
4.9 %
RANDOM
Rwork
0.1139
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obs
0.11624
92098
99.97 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK