Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 100 mM MES buffer, pH 6.5, 26-28% PEG-MME 2000, 200 mM ammonium sulfate and 20 mM 2-mercaptoethanol, vapor diffusion, temperature 298K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector
Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.8→55 Å / Num. obs: 33424 / % possible obs: 93.2 % / Biso Wilson estimate: 30.11 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)
Rmerge(I) obs
Diffraction-ID
% possible all
1.8-1.85
0.426
1
78.3
1.85-1.91
0.358
1
90.8
1.91-1.98
0.28
1
92
1.98-2.06
0.199
1
92.7
2.06-2.15
0.136
1
93
2.15-2.27
0.109
1
93.8
2.27-2.41
0.088
1
94.3
2.41-2.6
0.072
1
95
2.6-2.86
0.057
1
95.7
2.86-3.27
0.045
1
97
3.27-4.12
0.035
1
97.5
4.12-55
0.026
1
97.9
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Processing
Software
Name
Version
Classification
NB
SCALEPACK
datascaling
BUSTER-TNT
BUSTER2.11.1
refinement
PDB_EXTRACT
3.11
dataextraction
BUSTER
2.11.1
refinement
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9393 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.208
1424
5.06 %
RANDOM
Rwork
0.183
-
-
-
obs
0.1843
28123
92.87 %
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Displacement parameters
Biso mean: 34.59 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.4872 Å2
0 Å2
-1.7988 Å2
2-
-
-4.6546 Å2
0 Å2
3-
-
-
1.1674 Å2
Refine analyze
Luzzati coordinate error obs: 0.22 Å
Refinement step
Cycle: LAST / Resolution: 1.9→27.1 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2790
0
70
208
3068
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2960
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.94
4035
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1340
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
73
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
456
HARMONIC
5
X-RAY DIFFRACTION
t_it
2960
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.14
X-RAY DIFFRACTION
t_other_torsion
2.84
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
372
SEMIHARMONIC
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
3610
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.9→1.97 Å / Total num. of bins used: 14
Rfactor
Num. reflection
% reflection
Rfree
0.2594
112
4.19 %
Rwork
0.2343
2563
-
all
0.2353
2675
-
obs
-
-
92.87 %
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
-0.3029
0.3103
-0.0632
0.5543
-0.0538
2.731
-0.0072
-0.0006
-0.0049
0.1034
-0.0323
-0.0298
-0.0901
0.0545
0.0395
-0.0451
0.025
-0.0263
0.0201
-0.0262
-0.0563
16.0716
4.3037
25.1177
2
1.7904
-0.4711
0.2362
0.4354
0.0587
0.6038
0.0333
0.1697
0.1103
-0.0291
-0.0301
0.0051
0.0345
-0.0077
-0.0032
-0.044
0.0017
0.0289
-0.0419
0.0226
-0.0274
5.2396
-0.6107
0.0977
3
0.1243
0.0848
-0.1805
0.3615
0.3392
0.345
-0.0002
-0.0035
-0.0171
0.023
0.0062
-0.0183
0.0267
-0.0223
-0.0059
-0.0268
0.0238
0.0165
0.0454
-0.0654
-0.0323
6.3077
-2.9711
32.6584
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{A|9 - 107}
A
9 - 107
2
X-RAY DIFFRACTION
2
{A|108 - 328}
A
108 - 328
3
X-RAY DIFFRACTION
3
{A|329 - 356}
A
329 - 356
+
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