- PDB-3hok: X-ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2... -
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Basic information
Entry
Database: PDB / ID: 3hok
Title
X-ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: A Novel, Inducible Binding Mode
Journal: J.Med.Chem. / Year: 2009 Title: X-ray crystal structure of human heme oxygenase-1 with (2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: a novel, ...Title: X-ray crystal structure of human heme oxygenase-1 with (2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: a novel, inducible binding mode. Authors: Rahman, M.N. / Vlahakis, J.Z. / Vukomanovic, D. / Szarek, W.A. / Nakatsu, K. / Jia, Z.
Resolution: 2.19→43.42 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.412 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28894
1018
5.2 %
RANDOM
Rwork
0.22207
-
-
-
obs
0.22567
18614
88.4 %
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all
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19633
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-
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: 37.644 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.78 Å2
0 Å2
-1.38 Å2
2-
-
-3.33 Å2
0 Å2
3-
-
-
0.32 Å2
Refinement step
Cycle: LAST / Resolution: 2.19→43.42 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3498
0
118
186
3802
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
3715
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.047
2.046
5053
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.394
5
427
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.112
23.889
180
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.076
15
637
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19
15
26
X-RAY DIFFRACTION
r_chiral_restr
0.075
0.2
527
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2839
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.504
1.5
2147
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.934
2
3457
X-RAY DIFFRACTION
r_scbond_it
1.124
3
1568
X-RAY DIFFRACTION
r_scangle_it
1.883
4.5
1596
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.19→2.244 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.329
41
-
Rwork
0.234
799
-
obs
-
840
52.4 %
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