Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop Details: NANODROP, 23.1% PEG 3350, 0.214M Sodium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.95→35.267 Å / Num. obs: 15859 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.87 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.95
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.95-2.02
0.263
7.2
10958
1715
1
99.9
2.02-2.1
0.184
10.3
11201
1682
1
100
2.1-2.2
0.139
12.5
11510
1774
1
99.4
2.2-2.31
0.116
11
1258
332
1
20.5
2.31-2.46
0.089
17.8
12123
1782
1
100
2.46-2.65
0.072
20.3
11729
1716
1
100
2.65-2.91
0.061
23.9
11487
1687
1
100
2.91-3.33
0.05
27.9
11750
1732
1
100
3.33-4.19
0.045
29.7
10501
1618
1
92.2
4.19-35.267
0.038
31.6
11707
1822
1
99.3
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0067
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.95→35.267 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.184 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.159 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. THE REFLECTIONS WITHIN RESOLUTION RANGES 3.70-3.64 AND 2.3-2.2 ANGSTROM WERE EXCLUDED DURING INTEGRATION AND SUBSEQUENT STEPS DUE TO THE PRESENCE OF ICE RINGS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.218
792
5 %
RANDOM
Rwork
0.165
-
-
-
obs
0.167
15859
91.63 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 19.647 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.15 Å2
-0.07 Å2
0 Å2
2-
-
-0.15 Å2
0 Å2
3-
-
-
0.22 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→35.267 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1571
0
0
288
1859
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
1676
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1163
X-RAY DIFFRACTION
r_angle_refined_deg
1.41
1.978
2297
X-RAY DIFFRACTION
r_angle_other_deg
1.582
3
2827
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.398
5
225
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.374
23.125
80
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.361
15
272
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.496
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.085
0.2
255
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
1923
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
344
X-RAY DIFFRACTION
r_mcbond_it
1.808
3
1058
X-RAY DIFFRACTION
r_mcbond_other
0.502
3
424
X-RAY DIFFRACTION
r_mcangle_it
2.979
5
1696
X-RAY DIFFRACTION
r_scbond_it
4.616
8
618
X-RAY DIFFRACTION
r_scangle_it
6.9
11
591
LS refinement shell
Resolution: 1.95→2.001 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.249
68
-
Rwork
0.187
1182
-
all
-
1250
-
obs
-
-
99.76 %
Refinement TLS params.
Method: refined / Origin x: 22.5935 Å / Origin y: 12.4151 Å / Origin z: 38.2847 Å
11
12
13
21
22
23
31
32
33
T
-0.0172 Å2
0.0401 Å2
0.0308 Å2
-
-0.0276 Å2
0.0171 Å2
-
-
-0.0186 Å2
L
0.3968 °2
0.1923 °2
0.0372 °2
-
0.3713 °2
-0.139 °2
-
-
0.3999 °2
S
-0.0073 Å °
0.0128 Å °
0.0895 Å °
-0.0321 Å °
0.0305 Å °
0.0572 Å °
-0.0202 Å °
-0.0292 Å °
-0.0232 Å °
+
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