AUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
-
Components
#1: Protein
PutativeAcetyltransferase /
Mass: 33624.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: NP_142035.1, PH0012 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O57768
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: 2.25→29.037 Å / Num. obs: 22597 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.144 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 4.9
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
2.25-2.31
7.3
0.815
0.9
12110
1648
0.815
100
2.31-2.37
7.4
0.735
1
11717
1593
0.735
100
2.37-2.44
7.3
0.609
1.3
11464
1561
0.609
100
2.44-2.52
7.4
0.528
1.4
11056
1499
0.528
100
2.52-2.6
7.3
0.473
1.6
10694
1460
0.473
100
2.6-2.69
7.3
0.408
1.9
10403
1417
0.408
100
2.69-2.79
7.3
0.326
2.3
10162
1384
0.326
100
2.79-2.9
7.3
0.254
3
9756
1329
0.254
100
2.9-3.03
7.3
0.195
3.8
9261
1270
0.195
100
3.03-3.18
7.3
0.149
4.9
8940
1227
0.149
100
3.18-3.35
7.3
0.119
6.1
8482
1168
0.119
100
3.35-3.56
7.2
0.106
6.4
8013
1108
0.106
100
3.56-3.8
7.2
0.094
7.1
7434
1035
0.094
100
3.8-4.11
7.1
0.082
7.8
6981
978
0.082
100
4.11-4.5
7.1
0.068
9
6388
903
0.068
100
4.5-5.03
7.1
0.066
9.4
5853
830
0.066
100
5.03-5.81
7
0.071
9.3
5169
743
0.071
100
5.81-7.12
6.8
0.076
8.4
4322
638
0.076
100
7.12-10.06
6.5
0.058
9.9
3296
507
0.058
100
10.06-29.04
5.8
0.06
10.1
1725
299
0.06
96
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3.004
dataextraction
MOSFLM
datareduction
autoSHARP
phasing
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.25→29.037 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.298 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.176 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). ONE COENZYME A (COA) MONOMER WAS MODELED BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY. (5). ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO SOLUTION WERE MODELED. (6). RESIDUES -5 THROUGH -11 OF THE N-TERMINAL PURIFICATION TAG ARE LOCATED IN POOR DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.221
1154
5.1 %
RANDOM
Rwork
0.168
-
-
-
obs
0.171
22552
99.92 %
-
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: 31.366 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.8 Å2
0 Å2
0 Å2
2-
-
-1.8 Å2
0 Å2
3-
-
-
3.6 Å2
Refinement step
Cycle: LAST / Resolution: 2.25→29.037 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2253
0
68
175
2496
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2446
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1756
X-RAY DIFFRACTION
r_angle_refined_deg
1.635
2.001
3301
X-RAY DIFFRACTION
r_angle_other_deg
0.957
3
4236
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.586
5
296
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.615
22.566
113
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.522
15
438
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.683
15
25
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
345
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2700
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
528
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
436
X-RAY DIFFRACTION
r_nbd_other
0.203
0.2
1862
X-RAY DIFFRACTION
r_nbtor_refined
0.182
0.2
1163
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
1342
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.147
0.2
148
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.16
0.2
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.317
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.139
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
2.035
3
1585
X-RAY DIFFRACTION
r_mcbond_other
0.473
3
589
X-RAY DIFFRACTION
r_mcangle_it
2.894
5
2330
X-RAY DIFFRACTION
r_scbond_it
5.384
8
1104
X-RAY DIFFRACTION
r_scangle_it
6.637
11
971
LS refinement shell
Resolution: 2.25→2.308 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.28
86
-
Rwork
0.232
1561
-
all
-
1647
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: 29.3437 Å / Origin y: 4.7224 Å / Origin z: -0.1209 Å
11
12
13
21
22
23
31
32
33
T
-0.0831 Å2
0.0092 Å2
0.0173 Å2
-
-0.0627 Å2
-0.0316 Å2
-
-
-0.0812 Å2
L
0.955 °2
0.0521 °2
0.0092 °2
-
2.1622 °2
0.3372 °2
-
-
0.6468 °2
S
-0.0525 Å °
-0.0461 Å °
-0.0518 Å °
0.036 Å °
-0.0001 Å °
-0.042 Å °
0.0176 Å °
-0.0068 Å °
0.0526 Å °
+
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