Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.82 Å3/Da / Density % sol: 32.57 %
Crystal grow
Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: The crystallisation condition used is Index 71 (Cat. No.: HR2-944-71; Hampton Research, Aliso Viejo, CA, USA) containing 0.1 M BIS-TRIS pH 6.5, 0.2 M NaCl and 25% w/v Polyethylene glycol 3350.
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
Serial crystal experiment
1
100
1
N
2
80
1
N
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
ESRF
MASSIF-1
1
0.96546
SYNCHROTRON
Diamond
I23
2
2.7552
Detector
Type
ID
Detector
Date
DECTRIS PILATUS3 2M
1
PIXEL
Jul 21, 2023
DECTRIS PILATUS 12M
2
PIXEL
Jul 7, 2023
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.96546
1
2
2.7552
1
Reflection
Entry-ID: 8RF5
Resolution (Å)
Num. obs
% possible obs (%)
Redundancy (%)
CC1/2
Rmerge(I) obs
Rpim(I) all
Rrim(I) all
Diffraction-ID
Net I/σ(I)
1.098-35.647
40695
99.6
23.4
0.988
0.267
0.056
0.273
1
7.2
1.8-140.52
8084
84.2
15.2
0.998
0.08
0.02
2
32.8
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique obs
CC1/2
Rpim(I) all
Rrim(I) all
Diffraction-ID
% possible all
Mean I/σ(I) obs
1.098-1.117
19.8
3.85
2017
0.394
0.868
3.951
1
100
1.8-1.83
7.9
0.295
340
0.922
0.108
0.316
2
73
9.7
-
Processing
Software
Name
Version
Classification
PHENIX
(1.20.1-4487-000)
refinement
Aimless
Version0.7.9
datascaling
XDS
Jan10, 2022BUILT=20220820
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→35.645 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.31 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2016
2047
5.03 %
Rwork
0.1721
-
-
obs
0.1735
40662
99.49 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.1→35.645 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
927
0
0
90
1017
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
977
X-RAY DIFFRACTION
f_angle_d
1.227
1332
X-RAY DIFFRACTION
f_dihedral_angle_d
9.558
139
X-RAY DIFFRACTION
f_chiral_restr
0.092
155
X-RAY DIFFRACTION
f_plane_restr
0.008
175
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.1-1.12
0.3485
129
0.3404
2513
X-RAY DIFFRACTION
100
1.12-1.15
0.2838
171
0.2687
2506
X-RAY DIFFRACTION
99
1.15-1.18
0.2694
134
0.2208
2540
X-RAY DIFFRACTION
100
1.18-1.22
0.2546
119
0.2066
2526
X-RAY DIFFRACTION
100
1.22-1.26
0.2607
131
0.2155
2527
X-RAY DIFFRACTION
100
1.26-1.3
0.2548
151
0.2106
2538
X-RAY DIFFRACTION
100
1.3-1.35
0.2228
127
0.1647
2561
X-RAY DIFFRACTION
100
1.35-1.42
0.196
147
0.1587
2567
X-RAY DIFFRACTION
100
1.42-1.49
0.1979
129
0.1537
2558
X-RAY DIFFRACTION
100
1.49-1.58
0.1889
135
0.1444
2579
X-RAY DIFFRACTION
100
1.58-1.71
0.1574
135
0.1527
2580
X-RAY DIFFRACTION
100
1.71-1.88
0.2071
119
0.157
2627
X-RAY DIFFRACTION
100
1.88-2.15
0.2009
152
0.1621
2606
X-RAY DIFFRACTION
100
2.15-2.71
0.2057
135
0.1833
2670
X-RAY DIFFRACTION
100
2.71-35.645
0.1866
133
0.1664
2717
X-RAY DIFFRACTION
95
+
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