BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
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.
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
0.91837
1
2
0.97937
1
3
0.97916
1
Reflection
Resolution: 1.85→28.548 Å / Num. obs: 48739 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 14
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.85-1.9
7.3
0.896
2.3
25952
3552
0.896
100
1.9-1.95
7.3
0.738
1
25308
3458
0.738
100
1.95-2.01
7.3
0.565
1.4
24663
3362
0.565
100
2.01-2.07
7.3
0.464
1.7
23867
3255
0.464
100
2.07-2.14
7.3
0.375
2
23658
3222
0.375
100
2.14-2.21
7.3
0.299
2.5
22511
3066
0.299
100
2.21-2.29
7.3
0.255
3
21853
2980
0.255
100
2.29-2.39
7.3
0.203
3.7
21056
2870
0.203
100
2.39-2.49
7.3
0.175
4.3
20122
2752
0.175
100
2.49-2.62
7.3
0.149
4.9
19420
2657
0.149
100
2.62-2.76
7.3
0.128
5.5
18295
2518
0.128
100
2.76-2.93
7.3
0.116
5.8
17221
2371
0.116
100
2.93-3.13
7.3
0.096
6.9
16283
2245
0.096
100
3.13-3.38
7.2
0.079
8.2
15180
2103
0.079
100
3.38-3.7
7.2
0.065
9.4
14071
1951
0.065
100
3.7-4.14
7.2
0.055
11.1
12712
1766
0.055
100
4.14-4.78
7.1
0.056
11.1
11189
1576
0.056
100
4.78-5.85
7.1
0.055
10.9
9509
1348
0.055
100
5.85-8.27
6.9
0.044
14.6
7320
1067
0.044
100
8.27-28.548
6.3
0.039
15.1
3919
620
0.039
97.6
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.85→28.548 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.584 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 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. CALCIUM IONS, UNKNOWN LIGAND, POLYETHYLENE GLYCOL AND ETHYLENE GLYCOL MOLECULES ARE MODELED IN THE STRUCTURE. 5. RESIDUES 0, 1, 186 AND 187 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.188
2458
5 %
RANDOM
Rwork
0.158
-
-
-
obs
0.16
48690
99.95 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 25.14 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.94 Å2
0.47 Å2
0 Å2
2-
-
0.94 Å2
0 Å2
3-
-
-
-1.41 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→28.548 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2773
0
68
333
3174
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2991
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2049
X-RAY DIFFRACTION
r_angle_refined_deg
1.686
1.968
4067
X-RAY DIFFRACTION
r_angle_other_deg
1.019
3
4995
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.621
5
366
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.898
23.937
127
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.128
15
459
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.289
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.107
0.2
431
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
3314
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
616
X-RAY DIFFRACTION
r_nbd_refined
0.215
0.3
573
X-RAY DIFFRACTION
r_nbd_other
0.193
0.3
2133
X-RAY DIFFRACTION
r_nbtor_refined
0.187
0.5
1457
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.5
1473
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.205
0.5
432
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.104
0.5
1
X-RAY DIFFRACTION
r_metal_ion_refined
0.291
0.5
3
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.2
0.3
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.208
0.3
27
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.248
0.5
32
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.066
0.5
1
X-RAY DIFFRACTION
r_mcbond_it
2.059
3
1872
X-RAY DIFFRACTION
r_mcbond_other
0.526
3
721
X-RAY DIFFRACTION
r_mcangle_it
2.974
5
2921
X-RAY DIFFRACTION
r_scbond_it
4.449
8
1359
X-RAY DIFFRACTION
r_scangle_it
6.341
11
1146
LS refinement shell
Resolution: 1.85→1.898 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.29
176
-
Rwork
0.243
3380
-
all
-
3556
-
obs
-
-
99.97 %
Refinement TLS params.
Method: refined / Origin x: 44.796 Å / Origin y: 32.722 Å / Origin z: 14.48 Å
11
12
13
21
22
23
31
32
33
T
-0.0599 Å2
-0.0186 Å2
0.007 Å2
-
-0.0226 Å2
-0.0243 Å2
-
-
-0.1573 Å2
L
0.5262 °2
0.0195 °2
0.0106 °2
-
0.4994 °2
0.313 °2
-
-
1.6878 °2
S
-0.0165 Å °
0.0573 Å °
-0.0276 Å °
0.0063 Å °
-0.0706 Å °
0.1382 Å °
0.1543 Å °
-0.2635 Å °
0.0871 Å °
+
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