Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION
-
Sample preparation
Crystal
Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % / Description: NONE
-
Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: ROTATING ANODE / Wavelength: 1.54
Detector
Type: RIGAKU CCD / Detector: CCD
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 2.57→99.48 Å / Num. obs: 22994 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 64.23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shell
Resolution: 2.57→2.71 Å / % possible all: 97.1
-
Processing
Software
Name
Version
Classification
BUSTER
2.11.2
refinement
XDS
datareduction
Refinement
Method to determine structure: OTHER / Resolution: 2.57→28.41 Å / Cor.coef. Fo:Fc: 0.9395 / Cor.coef. Fo:Fc free: 0.9013 / SU R Cruickshank DPI: 0.552 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.531 / SU Rfree Blow DPI: 0.296 / SU Rfree Cruickshank DPI: 0.301
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2556
1182
5.17 %
RANDOM
Rwork
0.1924
-
-
-
obs
0.1955
22863
95.61 %
-
Displacement parameters
Biso mean: 55.83 Å2
Baniso -1
Baniso -2
Baniso -3
1-
7.3553 Å2
0 Å2
0.1216 Å2
2-
-
-13.5285 Å2
0 Å2
3-
-
-
6.1731 Å2
Refine analyze
Luzzati coordinate error obs: 0.378 Å
Refinement step
Cycle: LAST / Resolution: 2.57→28.41 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4399
0
108
143
4650
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
4706
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.12
6435
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1598
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
98
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
673
HARMONIC
5
X-RAY DIFFRACTION
t_it
4706
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.81
X-RAY DIFFRACTION
t_other_torsion
17.78
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
590
SEMIHARMONI
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
5427
SEMIHARMONI
4
LS refinement shell
Resolution: 2.57→2.69 Å / Total num. of bins used: 11
Rfactor
Num. reflection
% reflection
Rfree
0.2973
154
5.19 %
Rwork
0.2122
2812
-
all
0.2168
2966
-
obs
-
-
95.61 %
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
2.5824
-0.1935
-0.4332
0.4991
-0.2625
1.327
0.148
0.0421
0.2134
-0.1194
-0.0828
0.0366
-0.1092
0.072
-0.0652
-0.1359
0.0193
0.0153
-0.0004
0.0329
-0.1992
81.1353
-2.5209
18.3112
2
4.1336
-0.8794
0.0366
1.344
0.5067
1.0254
0.2646
0.3504
-0.2901
0.035
-0.3013
0.0857
0.0926
-0.0184
0.0367
-0.1372
0.0515
-0.0485
-0.0193
-0.0183
-0.1925
34.2431
2.0786
13.8347
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|* }
2
X-RAY DIFFRACTION
2
{ B|* }
+
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