BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 4, 2007 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91162
1
2
0.97941
1
3
0.97905
1
Reflection
Resolution: 1.7→29.086 Å / Num. obs: 86578 / % possible obs: 95 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.23 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.95
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.7-1.76
0.492
1.4
10444
15880
1
93.6
1.76-1.83
0.401
1.7
10766
16246
1
94.5
1.83-1.91
0.321
2.2
10494
15774
1
94.7
1.91-2.02
0.227
3.1
11925
17880
1
95.1
2.02-2.14
0.155
4.3
10298
15502
1
95.3
2.14-2.31
0.116
5.8
11375
16921
1
95.3
2.31-2.54
0.087
7.5
10934
16205
1
95.4
2.54-2.9
0.066
9.4
10954
16210
1
95.6
2.9-3.66
0.039
13.9
11535
16719
1
95.9
3.66-29.086
0.026
19.8
11604
16462
1
95
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
SHELXD
phasing
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.7→29.086 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.982 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.097 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. UNUSUAL NEGATIVE AND POSITIVE DENSITIES WERE PRESENT NEAR MSE RESIDUES 191 AND 225 OF A, B AND C SUBUNITS. 5. UNEXPLAINED ELECTRON DENSITIES NEAR RESIDUES 151 OF B AND C SUBUNITS WERE NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.193
4333
5 %
RANDOM
Rwork
0.154
-
-
-
obs
0.156
86554
98.99 %
-
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: 13.832 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.09 Å2
0 Å2
0.3 Å2
2-
-
0.18 Å2
0 Å2
3-
-
-
-0.13 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→29.086 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5908
0
0
943
6851
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
6180
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
4252
X-RAY DIFFRACTION
r_angle_refined_deg
1.509
1.976
8425
X-RAY DIFFRACTION
r_angle_other_deg
1.07
3
10321
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.988
5
781
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.085
22.737
274
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.462
15
1013
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.522
15
57
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
941
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
6956
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1293
X-RAY DIFFRACTION
r_nbd_refined
0.225
0.2
1534
X-RAY DIFFRACTION
r_nbd_other
0.195
0.2
4694
X-RAY DIFFRACTION
r_nbtor_refined
0.176
0.2
3057
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
2909
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.17
0.2
737
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.159
0.2
17
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.189
0.2
56
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.145
0.2
23
X-RAY DIFFRACTION
r_mcbond_it
2.115
3
4282
X-RAY DIFFRACTION
r_mcbond_other
0.57
3
1547
X-RAY DIFFRACTION
r_mcangle_it
2.575
5
6216
X-RAY DIFFRACTION
r_scbond_it
4.525
8
2537
X-RAY DIFFRACTION
r_scangle_it
6.327
11
2209
LS refinement shell
Resolution: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.279
297
-
Rwork
0.234
6050
-
obs
-
6347
98.63 %
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
0.2044
-0.0609
-0.0175
0.2961
-0.0287
0.1647
0.0128
-0.0018
-0.0021
0.0771
0.0061
-0.0037
0.0227
0.0006
-0.0189
-0.0066
-0.0019
-0.0042
-0.0319
0.0021
-0.0268
24.6781
28.8903
35.8457
2
0.2436
-0.1228
-0.0259
0.3048
0.1343
0.3334
0.0072
0.0635
0.0968
0.0254
0.0021
-0.0043
-0.0568
0.0124
-0.0093
-0.0292
-0.0007
0.0092
-0.0215
0.0244
-0.0069
25.4877
47.132
23.8079
3
0.4757
0.0216
-0.0486
0.346
-0.0409
0.2948
0.0175
0.1614
-0.0031
-0.0263
-0.0078
0.0072
0.0525
0.0245
-0.0097
-0.0347
0.0095
-0.0052
0.0044
-0.0034
-0.0506
23.4874
27.2564
13.4167
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
0 - 257
1 - 258
2
X-RAY DIFFRACTION
2
B
B
6 - 254
7 - 255
3
X-RAY DIFFRACTION
3
C
C
6 - 254
7 - 255
+
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