Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
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Details
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: 3.34 Å3/Da / Density % sol: 63.17 %
Type: MAR MAR325 / Detector: CCD / Date: Mar 12, 2010
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97907 Å / Relative weight: 1
Reflection
Resolution: 1.96→48.826 Å / Num. obs: 41141 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.33 Å2
Reflection shell
Resolution: 1.96→2.03 Å / Rmerge(I) obs: 1.546 / Mean I/σ(I) obs: 1.7 / % possible all: 100
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
BUSTER-TNT
BUSTER2.8.0
refinement
XSCALE
datascaling
PDB_EXTRACT
3.1
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
BUSTER
2.8.0
refinement
Refinement
Method to determine structure: SAD / Resolution: 1.96→48.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 Details: 1.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 ...Details: 1.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. 2.1,4-BUTANEDIOL (BU1), CHLORIDE (CL), ETHYLENE GLYCOL (EDO) AND ACETATE (ACT) MODELED ARE PRESENT PROTEIN/ CRYSTALLIZATION/CRYO BUFFER. 3.RESIDUES OF 8-106 OF CHAIN B ARE NOT WELL ORDERED, THE MODEL WAS GENERATED BASED ON A CHAIN. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor
Num. reflection
% reflection
Rfree
0.239
2066
5.02 %
Rwork
0.216
-
-
obs
0.217
41141
-
Displacement parameters
Biso mean: 55.26 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.96→48.83 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2850
0
40
283
3173
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
3008
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1
4096
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1384
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
81
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
422
HARMONIC
5
X-RAY DIFFRACTION
t_it
3008
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.03
X-RAY DIFFRACTION
t_other_torsion
2.73
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
409
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
3596
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.96→2.01 Å
Rfactor
Num. reflection
% reflection
Rfree
0.2452
171
5.69 %
Rwork
0.2281
2832
-
all
0.229
3003
-
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
2.6157
-0.1437
0.1018
1.5017
-0.6086
2.4455
0.143
0.1391
-0.2464
0.0355
0.0432
0.0698
0.1667
0.1338
-0.1861
-0.0705
0.0578
-0.0257
-0.0889
-0.0502
-0.1123
26.5674
54.1443
38.2051
2
2.9607
-0.5541
-1.0688
1.0726
-0.451
1.6411
0.2553
1.0885
0.722
-0.0301
-0.1494
-0.1006
-0.206
0.1723
-0.1059
-0.3804
0.0936
0.0263
0.4785
0.2413
-0.3188
20.0524
66.9352
11.8497
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{ A|8 - A|186 }
A
8 - 186
2
X-RAY DIFFRACTION
2
{ B|8 - B|186 }
B
8 - 186
+
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