Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 200 MM MES, 27% PEG8K, 200 MM AMMONIUM SULFATE, 1 MM MANGANESE CHLORIDE, 10 MM MAGNESIUM ACETATE, 10 MM TAURINE, AND 50 MM SODIUM FLUORIDE, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Monochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.1 Å / Relative weight: 1
Reflection
Resolution: 1.53→50.75 Å / Num. obs: 250493 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.2
Reflection shell
Resolution: 1.53→1.62 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7
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Processing
Software
Name
Version
Classification
CBASS
datacollection
PHENIX
(PHENIX.REFINE: 1.8.2_1309)
modelbuilding
PHENIX
(phenix.refine: 1.8.2_1309)
refinement
MOSFLM
datareduction
SCALA
datascaling
PHENIX
1.8.2_1309
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.534→46.9 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.1839
889
2 %
Rwork
0.1707
-
-
obs
0.1709
44527
99.52 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.534→46.9 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1657
0
7
225
1889
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.013
1728
X-RAY DIFFRACTION
f_angle_d
1.399
2335
X-RAY DIFFRACTION
f_dihedral_angle_d
14.263
655
X-RAY DIFFRACTION
f_chiral_restr
0.092
244
X-RAY DIFFRACTION
f_plane_restr
0.008
298
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.534-1.6301
0.2178
144
0.2092
7038
X-RAY DIFFRACTION
98
1.6301-1.756
0.1971
148
0.1788
7206
X-RAY DIFFRACTION
100
1.756-1.9327
0.194
147
0.1615
7258
X-RAY DIFFRACTION
100
1.9327-2.2124
0.191
148
0.1565
7263
X-RAY DIFFRACTION
100
2.2124-2.7873
0.1595
148
0.1708
7330
X-RAY DIFFRACTION
100
2.7873-46.9222
0.1867
154
0.1722
7543
X-RAY DIFFRACTION
100
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
4.8137
1.8646
-0.1736
4.0887
-1.5612
4.1791
-0.1437
0.2958
-0.1487
-0.1943
0.1161
0.0506
0.1995
-0.0635
0.0106
0.1788
-0.0347
0.0145
0.1958
-0.0287
0.1209
21.4684
18.8248
-18.3437
2
3.1489
2.1846
-1.9228
2.5645
-3.0708
7.7428
-0.0807
0.1704
-0.0663
-0.0813
0.0885
-0.0306
-0.0355
0.0338
0.0311
0.1843
-0.0565
-0.0104
0.141
-0.015
0.1708
17.8081
18.716
-8.7687
3
4.568
0.8343
-1.2495
8.5324
-4.3629
8.0116
0.3376
-1.0538
-0.9964
1.2379
-0.135
-0.1523
0.4213
-0.6936
0.0252
0.5109
-0.145
-0.0618
0.5259
0.1779
0.4122
14.5791
4.5757
10.1107
4
1.5694
0.637
-0.0967
3.6382
-2.8925
4.3268
0.2329
-0.1294
-0.5844
0.0671
-0.5355
-0.7253
0.4901
0.7211
0.1637
0.3111
-0.043
-0.0787
0.2733
0.1058
0.4008
14.5449
4.6028
0.8395
5
2.1546
-0.2212
0.3185
1.4149
0.8323
5.2604
0.2527
-0.2611
0.0151
0.1328
-0.2914
0.3567
0.3429
-0.7964
0.0089
0.1543
-0.0575
-0.0359
0.2259
0.0052
0.2109
3.6663
13.8237
-3.5046
6
5.236
-0.7536
-1.6822
8.7428
-2.1891
8.1638
0.0918
0.1527
0.6503
-0.0293
0.1804
1.0451
-0.5539
-0.854
-0.1911
0.2448
0.0322
-0.0122
0.2661
0.0041
0.3263
5.2113
26.3026
-1.066
7
2.4249
0.8441
-1.9725
0.7527
-0.3712
5.4031
0.0816
-0.0339
0.2654
-0.0251
-0.051
0.0754
-0.5381
0.2263
-0.0229
0.2115
-0.0766
-0.0295
0.1655
-0.0283
0.1914
20.8667
26.1661
-1.8345
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid -4 through 31 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid32through49 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid50through62 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid63through83 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid84through126 )
6
X-RAY DIFFRACTION
6
chain 'A' and (resid127through149 )
7
X-RAY DIFFRACTION
7
chain 'A' and (resid150through196 )
+
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