Mass: 18.015 Da / Num. of mol.: 1402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.3 Details: 0.1 M BICINE pH 9.3, 22% v/v PEG Smear Board, 50 mM glycine, raltitrexed (powder was added); 1 uL of this solution supplemented with 50% ethylene glycol was added to the drop with crystals for cryoprotection
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.977 Å
Detector
Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2021
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 1.23→55.15 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5 / Stereochemistry target values: ML Details: Hydrogen atoms at riding positions were added for refinement. B factor of non H atoms were refined anisotropically
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2294
1608
0.48 %
RANDOM
Rwork
0.1949
-
-
-
obs
0.195
332420
59.66 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.23→55.15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
14213
0
112
1402
15727
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
f_bond_d
0.011
X-RAY DIFFRACTION
f_angle_d
1.134
X-RAY DIFFRACTION
f_dihedral_angle_d
13.847
X-RAY DIFFRACTION
f_chiral_restr
0.077
X-RAY DIFFRACTION
f_plane_restr
0.011
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.23-1.27
0.2581
18
0.2271
3819
X-RAY DIFFRACTION
8
1.27-1.32
0.2612
37
0.2224
7643
X-RAY DIFFRACTION
15
1.32-1.37
0.2755
55
0.2178
12627
X-RAY DIFFRACTION
25
1.37-1.43
0.2265
82
0.2302
16538
X-RAY DIFFRACTION
33
1.43-1.51
0.2442
99
0.2242
22176
X-RAY DIFFRACTION
44
1.51-1.6
0.2251
149
0.2194
30163
X-RAY DIFFRACTION
60
1.6-1.73
0.2382
177
0.2153
38551
X-RAY DIFFRACTION
76
1.73-1.9
0.2881
242
0.2107
47640
X-RAY DIFFRACTION
95
1.9-2.18
0.2289
245
0.1949
50417
X-RAY DIFFRACTION
100
2.18-2.74
0.2237
258
0.197
50440
X-RAY DIFFRACTION
100
2.74-55.15
0.2163
246
0.1808
50798
X-RAY DIFFRACTION
100
+
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