Mass: 18.015 Da / Num. of mol.: 373 / 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.
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.69 Details: 0.17M di-ammonium hydrogen phosphate, 0.1M sodium acetate pH 4.69, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 1.65→29.907 Å / Num. obs: 28896 / % possible obs: 92.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.65-1.69
3.9
0.412
1.9
5830
1501
0.412
65.8
1.69-1.74
3.9
0.331
2.3
7293
1871
0.331
83.5
1.74-1.79
3.9
0.291
2.6
8196
2087
0.291
94.4
1.79-1.84
3.9
0.222
3.4
7985
2028
0.222
95.2
1.84-1.91
3.9
0.176
4.2
7562
1924
0.176
94.5
1.91-1.97
3.9
0.149
5
7409
1884
0.149
95.3
1.97-2.05
3.9
0.122
5.4
7177
1827
0.122
95.5
2.05-2.13
3.9
0.104
6.7
6997
1786
0.104
95.5
2.13-2.22
3.9
0.089
7.5
6724
1712
0.089
95.3
2.22-2.33
3.8
0.094
7.1
6073
1595
0.094
94.8
2.33-2.46
3.9
0.084
7.7
6054
1549
0.084
96.5
2.46-2.61
3.9
0.075
8.9
5661
1449
0.075
96.4
2.61-2.79
3.9
0.069
8.7
5449
1398
0.069
96.5
2.79-3.01
3.9
0.06
9.5
5017
1288
0.06
97.3
3.01-3.3
3.9
0.054
10.5
4719
1210
0.054
97
3.3-3.69
3.9
0.049
11.4
4091
1052
0.049
96.3
3.69-4.26
3.9
0.046
12.2
3747
970
0.046
97.5
4.26-5.22
3.9
0.044
14
3094
802
0.044
97.9
5.22-7.38
3.8
0.049
12.4
2353
621
0.049
97.8
7.38-29.91
3.6
0.053
10.5
1235
342
0.053
97.6
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0069
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3.004
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.65→29.907 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.12 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.118 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. ACETATE (ACT) IONS FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 4. UNEXPLAINED ELECTRON DENSITIES ON THE VAL 108 IN CHAINS A AND B WERE NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.224
1463
5.1 %
RANDOM
Rwork
0.175
-
-
-
obs
0.177
28896
92.74 %
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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: 12.38 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.5 Å2
-0.27 Å2
0.18 Å2
2-
-
0.72 Å2
0.35 Å2
3-
-
-
-0.34 Å2
Refinement step
Cycle: LAST / Resolution: 1.65→29.907 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2180
0
8
373
2561
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2274
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1549
X-RAY DIFFRACTION
r_angle_refined_deg
1.462
1.918
3063
X-RAY DIFFRACTION
r_angle_other_deg
1.398
3
3723
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.515
5
272
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.553
23.607
122
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.108
15
371
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
24.526
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
308
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2600
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
552
X-RAY DIFFRACTION
r_mcbond_it
1.709
3
1342
X-RAY DIFFRACTION
r_mcbond_other
0.417
3
562
X-RAY DIFFRACTION
r_mcangle_it
2.678
6
2152
X-RAY DIFFRACTION
r_scbond_it
4.531
8
932
X-RAY DIFFRACTION
r_scangle_it
6.314
11
911
LS refinement shell
Resolution: 1.65→1.693 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.362
81
-
Rwork
0.253
1420
-
all
-
1501
-
obs
-
-
65.83 %
+
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