Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.05 % Description: Flat plate like single crystals formed on Mylar surface. Other tested surfaces (glass, Kapton, poly propylene, poly ethylene, and COC) yielded poorly diffracting crystals, micro crystals, or poly-crystals.
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: Crystallization screening accomplished using combinatorial crystallization strategy. Separate libraries of precipitants, buffers, and additives were combinatorially combined with protein (11 ...Details: Crystallization screening accomplished using combinatorial crystallization strategy. Separate libraries of precipitants, buffers, and additives were combinatorially combined with protein (11 mg/mL protein in 10 mM Tris-HCL pH 7.0) in situ on the crystallization plate. Final concentrations of mother liquor: Buffer: 83 mM Sodium Citrate pH 4.0 Additives: 670 mM lithium sulfate, 8 mM L-glutamine, 8 mM L-Aspartic acid, 8 mM glycine, 8 mM trans-4-hydroxy-L-proline. Reservoir solution:Precipitant: 2 M lithium sulfate Crystals only grow on Mylar surface (many surfaces were tested).
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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: 2.34→110.31 Å / Num. obs: 29876 / % possible obs: 99.4 % / Redundancy: 4.73 % / CC1/2: 0.955 / Rmerge(I) obs: 0.335 / Net I/σ(I): 4.47
Reflection shell
Resolution: 2.34→2.4 Å / Rmerge(I) obs: 0.707 / Num. unique obs: 2116 / CC1/2: 0.622 / % possible all: 96.3
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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: 2.34→110.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.312 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22256
1483
5 %
RANDOM
Rwork
0.18192
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obs
0.18399
28375
99.36 %
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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