Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2 Å3/Da / Density % sol: 38.62 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% v / v MPD, 40 mM Na Cacodylate pH 7.0, 12 mM Spermine tetra-HCl, 80 mM Potassium Chloride and 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 1.6→50 Å / Num. all: 3147 / Num. obs: 3122 / % possible obs: 99.2 % / Redundancy: 22.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 49.77
Reflection shell
Resolution: 1.6→1.63 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 15.5 / Num. unique all: 141 / % possible all: 93.4
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Processing
Software
Name
Version
Classification
CBASS
datacollection
SHELXS
phasing
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.6→29.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.9 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22911
134
4.3 %
RANDOM
Rwork
0.18643
-
-
-
obs
0.18864
2965
99.04 %
-
all
-
2994
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 15.594 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.04 Å2
0 Å2
0 Å2
2-
-
-0.04 Å2
0 Å2
3-
-
-
0.08 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.097 Å
0.092 Å
Refinement step
Cycle: LAST / Resolution: 1.6→29.87 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
162
1
36
199
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.021
181
X-RAY DIFFRACTION
r_angle_refined_deg
1.531
3
277
X-RAY DIFFRACTION
r_chiral_restr
0.052
0.2
32
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
83
X-RAY DIFFRACTION
r_nbd_refined
0.139
0.2
62
X-RAY DIFFRACTION
r_nbtor_refined
0.273
0.2
107
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.177
0.2
22
X-RAY DIFFRACTION
r_metal_ion_refined
0.993
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.184
0.2
22
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.1
0.2
15
X-RAY DIFFRACTION
r_scbond_it
1.154
3
262
X-RAY DIFFRACTION
r_scangle_it
1.438
4.5
277
LS refinement shell
Resolution: 1.6→1.64 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.17
6
-
Rwork
0.215
192
-
obs
-
-
92.52 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
10.0892
1.4125
1.4568
0.1978
0.204
0.2103
0.0216
0.2862
-0.0008
-0.005
-0.0122
0.0101
-0.0585
-0.0434
-0.0093
-0.0025
0.0032
-0.0101
0.0025
-0.0051
-0.0204
40.6005
30.1718
-0.987
2
5.4551
-1.9288
-0.5311
3.1225
1.551
1.9382
0.0885
0.1148
0.0163
0.131
-0.0537
0.02
0.1055
-0.1385
-0.0348
-0.0549
0.0029
-0.0052
-0.0268
0.0172
-0.0473
25.3941
34.4537
-3.8004
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 9
2
X-RAY DIFFRACTION
2
A
5 - 13
+
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