Mass: 18.015 Da / Num. of mol.: 154 / 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 / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal grow
Method: vapor diffusion, sitting drop Details: 52.57 mg/mL MysmA.17112.a.A1 PS00688 in 25 mM Hepes pH 7.5, 0.5 M NaCl, 5% glycerol grown against JCSG+ screen conditions D2, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.5, 30% PEG 400 and soaked ...Details: 52.57 mg/mL MysmA.17112.a.A1 PS00688 in 25 mM Hepes pH 7.5, 0.5 M NaCl, 5% glycerol grown against JCSG+ screen conditions D2, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.5, 30% PEG 400 and soaked against 1.0 M NaI, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.0, 35% PEG 400 for 5 minutes, crystal tracking ID 217009d2, VAPOR DIFFUSION, SITTING DROP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Number: 214563 / Rmerge(I) obs: 0.068 / D res high: 1.95 Å / Num. obs: 32341 / % possible obs: 96.8
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
Num. obs
% possible obs (%)
ID
Rmerge(I) obs
1.95
2
2198
88.8
1
0.504
2
2.06
2197
91.7
1
0.393
2.06
2.12
2241
95
1
0.35
2.12
2.18
2180
96.4
1
0.27
2.18
2.25
2149
96.7
1
0.208
2.25
2.33
2041
97.1
1
0.185
2.33
2.42
2021
97.4
1
0.168
2.42
2.52
1940
97.6
1
0.153
2.52
2.63
1867
98.3
1
0.127
2.63
2.76
1778
98.4
1
0.103
2.76
2.91
1688
98.3
1
0.084
2.91
3.08
1608
99
1
0.069
3.08
3.3
1556
99.1
1
0.051
3.3
3.56
1394
99.2
1
0.04
3.56
3.9
1313
99.5
1
0.032
3.9
4.36
1163
99.7
1
0.029
4.36
5.04
1073
99.8
1
0.029
5.04
6.17
882
99.9
1
0.034
6.17
8.72
674
100
1
0.028
Reflection
Resolution: 1.95→50 Å / Num. all: 17898 / Num. obs: 17265 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 27.164 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.83
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.95-2
0.537
4
9363
1149
1
88.5
2-2.06
0.42
5.2
10158
1149
1
91.2
2.06-2.12
0.373
6.4
11278
1169
1
94.6
2.12-2.18
0.288
8.4
11829
1145
1
96
2.18-2.25
0.224
10.7
12315
1126
1
96.2
2.25-2.33
0.199
12.4
12523
1074
1
96.6
2.33-2.42
0.182
13.9
13368
1063
1
96.9
2.42-2.52
0.166
16.6
14774
1026
1
97
2.52-2.63
0.14
19.3
14399
986
1
97.8
2.63-2.76
0.119
22
13762
943
1
98
2.76-2.91
0.098
25
13091
898
1
97.7
2.91-3.08
0.083
28.5
12471
860
1
98.5
3.08-3.3
0.063
34.5
12020
837
1
98.8
3.3-3.56
0.053
41.6
10800
751
1
98.8
3.56-3.9
0.047
45.8
10119
714
1
99.2
3.9-4.36
0.044
49.5
8964
637
1
99.4
4.36-5.04
0.048
47.6
8250
599
1
99.7
5.04-6.17
0.062
43.9
6684
499
1
99.8
6.17-8.72
0.057
46.7
4962
394
1
100
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Phasing
Phasing
Method: SAD
Phasing MAD
D res high: 1.95 Å / D res low: 45.14 Å / FOM : 0.433 / FOM acentric: 0.464 / FOM centric: 0.215 / Reflection: 17200 / Reflection acentric: 15076 / Reflection centric: 2109
Phasing MAD shell
Resolution (Å)
FOM
FOM acentric
FOM centric
Reflection
Reflection acentric
Reflection centric
7.92-11.04
0.331
0.417
0.162
189
125
64
6.5-7.92
0.438
0.509
0.263
231
164
67
5.65-6.5
0.481
0.543
0.301
266
198
68
5.06-5.65
0.467
0.523
0.266
305
238
67
4.62-5.06
0.421
0.499
0.131
339
267
72
4.28-4.62
0.451
0.516
0.152
345
284
61
4.01-4.28
0.456
0.525
0.15
384
313
71
3.78-4.01
0.476
0.543
0.124
396
333
63
3.59-3.78
0.495
0.559
0.161
423
355
68
3.42-3.59
0.516
0.576
0.155
431
370
60
3.28-3.42
0.518
0.568
0.23
464
396
68
3.15-3.28
0.479
0.529
0.175
475
409
66
3.03-3.15
0.482
0.523
0.195
484
424
59
2.93-3.03
0.486
0.53
0.217
517
445
72
2.84-2.93
0.487
0.52
0.229
511
454
57
2.76-2.84
0.496
0.533
0.226
542
476
66
2.68-2.76
0.514
0.546
0.24
546
488
58
2.61-2.68
0.48
0.516
0.2
569
503
66
2.54-2.61
0.486
0.514
0.247
576
514
62
2.48-2.54
0.47
0.498
0.224
587
527
60
2.42-2.48
0.487
0.512
0.25
600
542
58
2.37-2.42
0.463
0.488
0.229
606
546
60
2.32-2.37
0.434
0.458
0.196
621
564
57
2.27-2.32
0.44
0.458
0.271
641
580
61
2.23-2.27
0.406
0.429
0.195
646
582
64
2.19-2.23
0.381
0.395
0.225
654
596
57
2.15-2.19
0.375
0.387
0.254
658
600
58
2.11-2.15
0.378
0.395
0.204
704
638
64
2.08-2.11
0.339
0.35
0.207
670
614
54
2.04-2.08
0.336
0.345
0.239
670
614
55
2.01-2.04
0.344
0.35
0.267
694
639
53
1.98-2.01
0.355
0.364
0.252
671
617
52
1.95-1.98
0.332
0.337
0.277
660
604
53
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Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
PHASER
EP
phasing
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
StructureStudio
datacollection
XDS
datareduction
Refinement
Method to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2147 / WRfactor Rwork: 0.1853 / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.849 / SU B: 6.411 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1659 / SU Rfree: 0.1525 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2358
876
5.1 %
RANDOM
Rwork
0.1966
-
-
-
obs
0.1985
17200
96.11 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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