Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.5 Å3/Da / Density % sol: 50.82 % Description: Most of the crystals grew in plates that poorly diffracted to 3 Angstrons , nevertheless after searching in many drops we could find more tridimensional crystals that diffracted up to 1 Angstrom
Crystal grow
Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Elution buffer (Size Exclusion): 50 mM Hepes pH 7.5, 50 mM NaCl, 1 mM DMSO Crystallization buffer: 17% PEG 6.000, 0.2 M calcium acetate
Resolution: 1.09151939067→40.4 Å / SU ML: 0.0898747422135 / Cross valid method: FREE R-VALUE / Phase error: 17.5736458365 Details: The data are >97% complete to 1.4A resolution. The low over all completeness is due to 68% completeness in the highest resolution shell (1.4-1.1A resolution
Rfactor
Num. reflection
% reflection
Rfree
0.159859886456
2000
1.82999359502 %
Rwork
0.150397880586
-
-
obs
0.150566354651
109290
81.8455501303 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 17.3294899896 Å2
Refinement step
Cycle: LAST / Resolution: 1.09151939067→40.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2296
0
54
480
2830
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.00914097867011
2521
X-RAY DIFFRACTION
f_angle_d
1.05328660683
3440
X-RAY DIFFRACTION
f_chiral_restr
0.374613677346
389
X-RAY DIFFRACTION
f_plane_restr
0.0067036751346
440
X-RAY DIFFRACTION
f_dihedral_angle_d
20.4064454927
930
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.0915-1.1188
0.294345463749
62
0.273842922882
3314
X-RAY DIFFRACTION
35.6306068602
1.1188-1.1491
0.268070864482
81
0.243758713686
4339
X-RAY DIFFRACTION
46.3993281545
1.1491-1.1829
0.222916579328
113
0.222757198725
6070
X-RAY DIFFRACTION
65.1184834123
1.1829-1.2211
0.214846772732
133
0.213038021783
7144
X-RAY DIFFRACTION
76.4471057884
1.2211-1.2647
0.198458138721
140
0.199025941427
7541
X-RAY DIFFRACTION
80.6065694197
1.2647-1.3154
0.19329300452
146
0.188588684079
7825
X-RAY DIFFRACTION
83.5359463425
1.3154-1.3752
0.195249848765
154
0.181288778515
8230
X-RAY DIFFRACTION
88.1227664494
1.3752-1.4477
0.182448285302
157
0.166788990355
8463
X-RAY DIFFRACTION
90.6795707974
1.4477-1.5384
0.167515356022
163
0.151908474498
8712
X-RAY DIFFRACTION
93.0976607574
1.5384-1.6572
0.155367220547
166
0.142058235881
8900
X-RAY DIFFRACTION
95.1711106446
1.6572-1.824
0.136298298816
168
0.141345075836
9054
X-RAY DIFFRACTION
96.3133159269
1.824-2.0879
0.154532377427
170
0.136071078013
9109
X-RAY DIFFRACTION
97.1216244505
2.0879-2.6305
0.144648645703
172
0.137309648637
9200
X-RAY DIFFRACTION
97.9924717691
2.6305-44.5701
0.147078822708
175
0.138208070879
9389
X-RAY DIFFRACTION
98.9959631508
Refinement TLS params.
Method: refined / Origin x: -38.1723037237 Å / Origin y: 86.9790978427 Å / Origin z: 63.5542836084 Å
11
12
13
21
22
23
31
32
33
T
0.0704159678563 Å2
0.00283531016019 Å2
-0.00215399651564 Å2
-
0.0628207465125 Å2
-0.0069517337931 Å2
-
-
0.0567405539019 Å2
L
0.338124862915 °2
0.0922346736372 °2
-0.0281506369245 °2
-
0.400602047252 °2
-0.251081397043 °2
-
-
0.242901152708 °2
S
0.0031115017437 Å °
0.0108923862725 Å °
0.003053850139 Å °
0.0112768471593 Å °
0.0307312010139 Å °
0.0187090548114 Å °
0.0123477432194 Å °
-0.0110298923265 Å °
0.029872760259 Å °
Refinement TLS group
Selection details: all
+
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