Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modification
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal grow
Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.8 M NaCl, 0.1 M Tris/HCl, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97923 Å / Relative weight: 1
Reflection
Resolution: 1.85→50 Å / Num. all: 14603 / Num. obs: 14408 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 25.6
Reflection shell
Resolution: 1.85→1.88 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.6 / Num. unique all: 707 / % possible all: 95.9
-
Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
SHELX
modelbuilding
MLPHARE
phasing
DM
modelbuilding
ARP/wARP
modelbuilding
Coot
modelbuilding
PHENIX
(phenix.refine: 1.6.4_486)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
SHELX
phasing
DM
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.85→25.932 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML Details: Hydrogen atoms have been added at ridding positions
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1908
1102
7.65 %
random
Rwork
0.1617
-
-
-
all
0.1639
14402
-
-
obs
0.1639
14402
98.8 %
-
Solvent computation
Shrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.816 Å2 / ksol: 0.482 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-0.0213 Å2
-0 Å2
0 Å2
2-
-
-0.0213 Å2
-0 Å2
3-
-
-
0.0426 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→25.932 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
876
0
16
78
970
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.015
941
X-RAY DIFFRACTION
f_angle_d
1.381
1282
X-RAY DIFFRACTION
f_dihedral_angle_d
14.957
343
X-RAY DIFFRACTION
f_chiral_restr
0.1
136
X-RAY DIFFRACTION
f_plane_restr
0.007
166
LS refinement shell
Refine-ID: X-RAY DIFFRACTION
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
% reflection obs (%)
1.8472-1.9313
0.2481
142
0.2143
1644
1644
98
1.9313-2.0331
0.2211
132
0.1751
1623
1623
98
2.0331-2.1604
0.1979
151
0.1579
1632
1632
99
2.1604-2.3271
0.1873
129
0.1557
1675
1675
99
2.3271-2.5611
0.2041
142
0.1611
1656
1656
99
2.5611-2.9313
0.2225
135
0.1862
1669
1669
99
2.9313-3.6914
0.188
139
0.1695
1673
1673
100
3.6914-25.935
0.1526
132
0.1359
1728
1728
99
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
1.132
0.6553
0.1689
0.656
-0.0911
0.1629
0.0772
0.0232
0.0171
0.1016
-0.0646
-0.0336
-0.0422
0.0468
-0.0055
0.1394
-0.0259
-0.014
0.1469
-0.0019
0.1319
4.2905
-34.0524
6.4667
2
0.5337
0.9601
-0.196
2.1653
0.0384
0.5018
0.2219
-0.1429
0.0967
0.4127
-0.2266
0.1306
-0.0274
0.06
0.0099
0.2685
-0.0551
-0.0083
0.175
-0.0221
0.1791
0.0861
-30.7172
12.6263
3
0.9737
0.4367
-0.1492
1.4248
-0.1879
0.1271
0.0363
-0.02
0.0192
0.0522
-0.0227
0.1638
0.0065
0.1066
0.0007
0.1176
0.0099
-0.0091
0.1481
-0.007
0.1075
-3.4849
-39.7442
8.8042
4
4.0479
-0.206
0.4253
2.5183
0.5433
0.1731
-0.0195
1.5556
0.1487
-0.8975
-0.1433
-0.0402
-0.3617
0.0968
0.1004
0.3642
0.0416
-0.0401
0.5147
-0.0015
0.1628
-2.977
-32.1733
-11.3643
5
2.6469
-0.4737
-0.2309
2.5167
-1.0767
2.0326
0.3772
0.4406
-0.2317
0.1695
-0.3317
-0.6202
-0.2645
-0.427
-0.0796
0.161
0.0767
-0.0138
0.1991
0.032
0.2645
-10.6832
-28.4979
-1.6035
6
3.6653
-0.8987
-0.3387
0.6872
-0.3289
0.4138
0.6882
1.0842
0.2594
-0.5075
-0.486
-0.1906
0.0165
0.0897
-0.1185
0.3393
0.1649
0.0817
0.4258
0.1151
0.3076
-12.1633
-24.3925
-9.0422
7
2.0933
2.3291
4.4376
3.0439
5.0093
9.4769
-0.3479
0.3841
-0.3494
0.195
0.03
0.1037
0.0099
0.4171
0.2088
0.2436
0.064
0.0337
0.3324
-0.0537
0.2011
-19.9386
-31.0991
-9.5811
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid1:23)
2
X-RAY DIFFRACTION
2
(chainAandresid24:39)
3
X-RAY DIFFRACTION
3
(chainAandresid40:64)
4
X-RAY DIFFRACTION
4
(chainAandresid65:78)
5
X-RAY DIFFRACTION
5
(chainAandresid79:96)
6
X-RAY DIFFRACTION
6
(chainAandresid97:107)
7
X-RAY DIFFRACTION
7
(chainAandresid108:111)
+
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