Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 ...Details: Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 mM DTT. Cryo: 75% Reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution: 2.1→40.26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.158 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26463
1833
5.1 %
RANDOM
Rwork
0.19709
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obs
0.2006
34021
98.61 %
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all
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35854
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 47.862 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.19 Å2
0 Å2
-0.01 Å2
2-
-
-0.16 Å2
0 Å2
3-
-
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-0.04 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→40.26 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3667
0
144
151
3962
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
3923
X-RAY DIFFRACTION
r_angle_refined_deg
1.512
1.998
5331
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.775
5
462
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.666
24.247
186
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.446
15
658
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.652
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
581
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2918
X-RAY DIFFRACTION
r_nbd_refined
0.208
0.2
1654
X-RAY DIFFRACTION
r_nbtor_refined
0.305
0.2
2707
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.135
0.2
213
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.202
0.2
14
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.192
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
1.818
3
2367
X-RAY DIFFRACTION
r_mcangle_it
2.616
4
3709
X-RAY DIFFRACTION
r_scbond_it
3.462
5
1748
X-RAY DIFFRACTION
r_scangle_it
4.756
7
1621
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20