Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal grow
Temperature: 291 K / Method: mircobatch under oil / pH: 8.5 Details: 100 mM TRIS (pH 8.5), 20% (v/v) PEG 3350, and 200 mM MgCl2 , mircobatch under oil, temperature 291K
Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.55 / Num. unique all: 3589 / Rsym value: 0.464 / % possible all: 100
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Processing
Software
Name
Version
Classification
PHENIX
(phenix.refine: 1.7_650)
refinement
SnB
phasing
RESOLVE
modelbuilding
XTALVIEW
refinement
ADSC
Quantum
datacollection
HKL-2000
datareduction
SCALEPACK
datascaling
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.393→48.79 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2461
1885
10.22 %
RANDOM
Rwork
0.1791
-
-
-
all
0.1866
35868
-
-
obs
0.1859
18450
99.38 %
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Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.647 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Biso mean: 41.7 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.8369 Å2
-0 Å2
-2.2861 Å2
2-
-
-1.4375 Å2
-0 Å2
3-
-
-
-0.3994 Å2
Refinement step
Cycle: LAST / Resolution: 2.393→48.79 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3159
0
32
90
3281
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
3255
X-RAY DIFFRACTION
f_angle_d
1.117
4404
X-RAY DIFFRACTION
f_dihedral_angle_d
15.325
1203
X-RAY DIFFRACTION
f_chiral_restr
0.074
490
X-RAY DIFFRACTION
f_plane_restr
0.004
567
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.393-2.4577
0.3358
120
0.2237
1181
X-RAY DIFFRACTION
93
2.4577-2.53
0.2742
146
0.2075
1284
X-RAY DIFFRACTION
100
2.53-2.6117
0.2861
141
0.1847
1265
X-RAY DIFFRACTION
100
2.6117-2.705
0.2903
158
0.1959
1284
X-RAY DIFFRACTION
100
2.705-2.8133
0.266
138
0.1935
1273
X-RAY DIFFRACTION
100
2.8133-2.9414
0.3393
154
0.1969
1274
X-RAY DIFFRACTION
100
2.9414-3.0964
0.2866
157
0.1888
1258
X-RAY DIFFRACTION
100
3.0964-3.2904
0.2382
147
0.1756
1274
X-RAY DIFFRACTION
100
3.2904-3.5443
0.2708
140
0.1785
1309
X-RAY DIFFRACTION
100
3.5443-3.9009
0.2108
154
0.1658
1280
X-RAY DIFFRACTION
100
3.9009-4.465
0.1987
128
0.1498
1289
X-RAY DIFFRACTION
100
4.465-5.6241
0.2316
148
0.1738
1289
X-RAY DIFFRACTION
100
5.6241-48.8241
0.222
154
0.1872
1305
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Origin x: -13.6155 Å / Origin y: -24.8997 Å / Origin z: -33.7711 Å
11
12
13
21
22
23
31
32
33
T
0.0967 Å2
-0.0129 Å2
-0.0085 Å2
-
0.1214 Å2
0.0034 Å2
-
-
0.1357 Å2
L
0.3435 °2
-0.0483 °2
-0.0397 °2
-
0.5055 °2
-0.1259 °2
-
-
0.7825 °2
S
0.0059 Å °
-0.048 Å °
0.035 Å °
0.0249 Å °
-0.0578 Å °
0.0049 Å °
-0.0843 Å °
-0.005 Å °
-0 Å °
Refinement TLS group
Selection details: all
+
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