Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
AUTHOR STATES THAT THE LONG BOND DISTANCE IN VO4 REFLECTS THAT THIS VANADATE IS A TRANSITION STATE ...AUTHOR STATES THAT THE LONG BOND DISTANCE IN VO4 REFLECTS THAT THIS VANADATE IS A TRANSITION STATE ANALOG WITH BIPYRAMIDAL GEOMETRY.IN THESE COMPLEXES THE AXIAL V-O BOND DISTANCES ARE MUCH LONGER THAN SEEN IN SIMPLE VO4 COMPLEXES.
Sequence details
THE SEQUENCE CONFLICTS ARE DUE TO VARIATIONS OF DIFFERENT VERSIONS OF THE WILD-TYPE DICTYOSTELIUM MYOSIN.
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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal grow
Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: mixing 5 ul of protein with an equal volume of well solution containing 100 mM MOPS, 250 mM MgCl2, 12% PEG 8000, 1 mM TCEP, and 2 mM Thymol, pH 7.0, vapor diffusion, hanging drop, temperature 278K
Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.329 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24479
2569
5.1 %
RANDOM
Rwork
0.19224
-
-
-
obs
0.19493
48034
99.11 %
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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: 34.536 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.3 Å2
0 Å2
0 Å2
2-
-
2.7 Å2
0 Å2
3-
-
-
-2.4 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5528
0
60
596
6184
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.022
5702
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.826
1.959
7722
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.278
5
708
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.685
24.8
275
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.307
15
951
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.489
15
28
X-RAY DIFFRACTION
r_chiral_restr
0.123
0.2
848
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
4349
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.211
0.2
2651
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.307
0.2
3899
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.207
0.2
503
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.323
0.2
2
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.226
0.2
46
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.299
0.2
13
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
1.147
1.5
3647
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.855
2
5639
X-RAY DIFFRACTION
r_scbond_it
2.817
3
2389
X-RAY DIFFRACTION
r_scangle_it
4
4.5
2081
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.2→2.256 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.326
167
-
Rwork
0.234
3332
-
obs
-
-
93.91 %
+
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