Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
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: 1.99→55 Å / Num. obs: 25736 / % possible obs: 98.2 % / Biso Wilson estimate: 28.93 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.2
Reflection shell
Resolution (Å)
Rmerge(I) obs
Diffraction-ID
% possible all
1.99-2.06
0.185
1
87.3
2.06-2.13
0.154
1
99.6
2.13-2.2
0.123
1
99.6
2.2-2.29
0.104
1
99.4
2.29-2.39
0.088
1
99.5
2.39-2.52
0.073
1
99.7
2.52-2.68
0.062
1
99.8
2.68-2.88
0.057
1
99.9
2.88-3.17
0.049
1
100
3.17-3.63
0.046
1
99.8
3.63-4.58
0.044
1
98.5
4.58-55
0.04
1
95.5
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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: 1.99→38.35 Å / Cor.coef. Fo:Fc: 0.9375 / Cor.coef. Fo:Fc free: 0.9068 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2245
1307
5.08 %
RANDOM
Rwork
0.1797
-
-
-
obs
0.182
25723
97.82 %
-
Displacement parameters
Biso mean: 33.54 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.1294 Å2
0 Å2
3.9091 Å2
2-
-
-3.9724 Å2
0 Å2
3-
-
-
1.843 Å2
Refine analyze
Luzzati coordinate error obs: 0.217 Å
Refinement step
Cycle: LAST / Resolution: 1.99→38.35 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2772
0
59
213
3044
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.009
2933
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.91
3986
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1342
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
69
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
455
HARMONIC
5
X-RAY DIFFRACTION
t_it
2933
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.89
X-RAY DIFFRACTION
t_other_torsion
2.81
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
373
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
3516
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.99→2.07 Å / Total num. of bins used: 13
Rfactor
Num. reflection
% reflection
Rfree
0.2247
123
4.8 %
Rwork
0.1839
2440
-
all
0.1859
2563
-
obs
-
-
97.82 %
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
-0.4887
1.0914
0.234
0.0476
0.9998
2.4199
0.0015
-0.0021
0.0043
0.062
0.0251
-0.0154
-0.0563
0.0466
-0.0266
0.0083
0.0818
-0.0614
0.0121
-0.0415
-0.0409
18.1051
3.8975
25.1682
2
1.6959
-0.84
0.9349
0.9546
-0.5281
1.3272
-0.0434
-0.0481
0.0752
-0.0017
0.0083
-0.0159
-0.0176
-0.0384
0.0351
-0.06
-0.0037
0.0194
-0.0606
-0.0165
-0.0179
4.0922
2.0232
2.344
3
0.032
-0.11
0.0067
0
-0.023
0.1375
-0.001
-0.0007
-0.0011
-0.0051
-0.0072
-0.0062
-0.0004
-0.0024
0.0082
0.005
0.0241
0.008
0.0157
0.0304
-0.0119
3.1167
4.9404
-16.0842
4
0.982
-0.8524
0.4179
1.2614
-0.4172
0.1744
0.0074
0.0429
-0.0282
-0.0556
-0.0058
0.0101
0.0436
0.0017
-0.0016
0.0017
0.0054
0.0094
-0.0136
-0.0144
-0.0164
9.3655
-9.0577
-3.0708
5
-0.1459
-0.0417
0.3218
0.4329
0.8849
0.49
-0.0002
-0.0032
-0.0056
0.0135
0.0032
-0.0028
0.0115
-0.0227
-0.003
0.0237
0.0133
-0.0489
0.0176
-0.042
-0.0371
5.7571
-1.5546
31.7077
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 - 267}
A
108 - 267
3
X-RAY DIFFRACTION
3
{A|268 - 275}
A
268 - 275
4
X-RAY DIFFRACTION
4
{A|276 - 327}
A
276 - 327
5
X-RAY DIFFRACTION
5
{A|328 - 354}
A
328 - 354
+
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