BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE 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 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
0.97883
1
3
0.97916
1
Reflection
Resolution: 1.7→28.262 Å / Num. obs: 12524 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.904 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 17.57
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
0.32
3.1
5495
2078
1
90.2
1.76-1.83
0.278
3.9
6840
2326
1
99.7
1.83-1.91
0.209
5.2
6679
2259
1
99.5
1.91-2.02
0.151
7.4
7481
2530
1
99.7
2.02-2.14
0.094
11.1
6531
2221
1
100
2.14-2.31
0.065
14.9
7062
2398
1
99.8
2.31-2.54
0.047
19.3
6858
2305
1
99.7
2.54-2.9
0.035
25.5
6758
2292
1
99.8
2.9-3.66
0.023
37.6
6918
2360
1
99.6
3.66-28.262
0.019
46.6
6674
2301
1
97.1
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.7→28.262 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.842 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.127 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. SEVEN PG4 AND ONE TRIS MOLECULE(S) HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.255
584
4.7 %
RANDOM
Rwork
0.202
-
-
-
obs
0.205
12479
99.3 %
-
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: 21.164 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.63 Å2
0 Å2
0 Å2
2-
-
-2.2 Å2
0 Å2
3-
-
-
1.58 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→28.262 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
814
0
67
65
946
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
923
X-RAY DIFFRACTION
r_bond_other_d
0.005
0.02
651
X-RAY DIFFRACTION
r_angle_refined_deg
1.814
2.004
1228
X-RAY DIFFRACTION
r_angle_other_deg
1.278
3
1622
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.652
5
117
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.205
27.179
39
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.86
15
174
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
0.679
15
1
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
138
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
968
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
153
X-RAY DIFFRACTION
r_nbd_refined
0.178
0.3
152
X-RAY DIFFRACTION
r_nbd_other
0.142
0.3
581
X-RAY DIFFRACTION
r_nbtor_refined
0.168
0.5
407
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.5
487
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.155
0.5
105
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.185
0.3
10
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.19
0.3
28
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.327
0.5
8
X-RAY DIFFRACTION
r_mcbond_it
2.223
3
616
X-RAY DIFFRACTION
r_mcbond_other
0.587
3
217
X-RAY DIFFRACTION
r_mcangle_it
2.785
5
900
X-RAY DIFFRACTION
r_scbond_it
5.278
8
405
X-RAY DIFFRACTION
r_scangle_it
7.28
11
320
LS refinement shell
Resolution: 1.7→1.746 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.313
40
-
Rwork
0.232
806
-
obs
-
846
94.42 %
Refinement TLS params.
Method: refined / Origin x: 13.8667 Å / Origin y: 1.0359 Å / Origin z: -17.3354 Å
11
12
13
21
22
23
31
32
33
T
-0.0782 Å2
-0.0022 Å2
-0.0022 Å2
-
-0.0539 Å2
0.0057 Å2
-
-
-0.0971 Å2
L
2.2766 °2
1.0335 °2
0.6794 °2
-
7.5134 °2
0.6823 °2
-
-
0.9009 °2
S
0.0003 Å °
0.0509 Å °
0.0319 Å °
-0.0027 Å °
0.0151 Å °
0.0581 Å °
-0.0533 Å °
-0.0555 Å °
-0.0155 Å °
+
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